You don’t get separate animate dead control pools from cleric and wizard, so you only get 32 HD, not 64. Undead from Rebuke Undead are in addition to this.

From the Revised Necromancer Handbook:

You are not going to play a True Necromancer!

A lot of people love the True Necromancer, even though it’s a completely crippled class. Even a Mystic Theurge is better, and that’s saying quite a bit because that class is a dog with fleas. You’re 5 real caster levels behind the curve. If you just took Leadership, and then your cohort took Leadership, both of the cohorts would have better casting than you (being 2 levels behind and 4 levels behind respectively). You can provide the party better and more powerful Necromancy as a single classed Fighter that happens to have Leadership than you would if you were a “True” Necromancer.

Top Ten Reasons True Necromancers Are Bad

1. At 14th level, you are five caster levels behind in both classes, so if the party Fighter took Leadership, and his cohort got Leadership, he’d actually be bringing more Necromancy to the table than you. As a fighter.

2. You have to take the Death Domain as a Necromancer Cleric, which is a waste of a Domain Slot when you are trying to be good at Necromancy.

3. In the early levels, you postpone your access to Animate Dead by 4 levels.

4. At 8th level a True Necromancer can create, but not control Ghouls. A Cleric at that level can control but not create Ghouls. Guess which is better? At 11th level, the True Necromancer gets the ability to control Ghouls, and the Cleric gets the ability to create them, so there’s no point at which this is advantageous.

5. The only unique ability of the True Necromancer class is unimpressive. Desecrate is a great spell, but it’s also a second level spell.

6. True Necromancers eventually get a bonus to Rebuking – at 17th level they have a +1 bonus to their Rebuking level. But at 7th level they have a 3 level penalty to their Rebuking level. So at low levels when rebuking is good they can’t use it, and at high levels when Rebuking doesn’t matter they don’t care.

7. True Necromancers are always going to have underwhelming Save DCs. Between MAD and the fact that they are often forced to use spells that are 3 spell levels lower than what the single-classed casters can use, they’re going to be out enough Save DC that it shows. A lot.

8. As a True Necromancer you have all the disadvantages of both a Cleric (the gods can take away all your spellcasting at any time), and a Wizard (you have Arcane Spell Failure, preventing you from wearing good armor). Also, your BAB and HPs stink when compared to a Cleric.

9. Control pools from Animate Dead actually don’t accumulate between your two classes. It’ right in the spell, if you cast the spell it considers all undead you control from all castings of Animate Dead, not just your Arcane or just your Divine castings of the spell. Some people say differently, and some even quote CustServ, but when was the last time you won an argument with your DM using the line "some guy on a board said that CustServ told him....."?

10. There is almost no synergy between Cleric and Wizard Necromancy. Any synergy you desperately want to find could be replicated by just taking the Apprentice feat at first level and having some Use Magic Device. Get yourself a couple of Wizard Scrolls or something. It’s a better buy than setting 5 caster levels on fire. Smart cookies can even get the right spell effects off monsters for free, no less.

Ultimately, even if you argue that the pools are separate and you get 64 HD worth, the loss of Caster Level makes that a wash compared to simply taking the Deathbound Domain (which gives 50% more rather than 100% more, but at far lower cost).

I strongly recommend either cleric or dread necromancer for the goal of having a big army of undead minions. Wizards can work too; they won’t be as good as cleric or dread necromancer for this purpose, but they’ll be a whole lot better than true necromancers.

It all comes down to agency. What choices are the players making?

If you are spoon-feeding them encounters, which they have no options but to engage, then yes, it's on you to make sure those encounters are survivable. If they are choosing what to do and what to engage, then the responsibility lies on their heads, not yours.

Let's look at two possible situations.

Situation 1

The PCs are in camp when some raiders attack. Oh noes! They wake up, but the raiders are surrounding them. They have no choice but to fight the raiders, and they are of such number and ability that at least one PC death is, essentially, inescapable.

Situation 2

The PCs are in a town when it is about to be attacked in force. They can stay and help the town defense, in which case it may stand. They may also flee the town, in which case the attackers will almost certainly win.

However, the attackers are of such force and number that if the PCs decide to stay and defend the city, it is highly likely that at least one of them will die.

Choice is the difference

In both of these scenarios, the PCs are faced with a fight that they might not survive. However, in the second one, they choose to get involved in that fight. It is their choice to risk their PCs to keep the town standing (or not). Not only does this put the responsibility on their head, but it also gives them a chance to be truly heroic. These types of choices (what am I willing to risk?) are some of the best moments in roleplaying, especially when real risk is on the table.

It's okay for PCs to die! But they should do so as a result of choices they make, not encounters that the GM "throws" at them.

Try a Clock

For the specific case in the OP, consider something like an Apocalypse World front's "clock". As the PCs engage in activities that will cause unwanted attention, you can increase the "clock" and the tension/heat that the players will encounter. This gives them an idea of the seriousness without making it an immediate "you die" moment. It also gives them the choice to continue with what they're doing or not.

So, for the "heresy" clock, the stages might look like this:

Stage 1: Mutterings of heresy. Some of the townsfolk talk about a new heresy they've been hearing.

Stage 2: Known heresy. People talk about this crazy new heresy they've heard about, with specifics.

Stage 3: Official pronouncements. There are proclamations that the heresy is in fact against the church.

Stage 4: Public trials/executions. Heretics are found and imprisoned or killed.

Stage 5: Manhunt. Wanted posters are put up for the lead heretics (aka the PCs). Movement becomes difficult.

Stage 6: Assassin squads. Exactly what it says on the tin.

You can then advance the current stage based on time or PC actions. This will give the impression of advancement and real change in the setting, give enough of a social movement to warrant the church's actions, and, perhaps most importantly, give the PCs plenty of warning that continuing on this path will result in dramatic consequences.

And that may be cool! This kind of "heresy plotline" may be exactly what the players want, and so letting them play through that may totally make them happy.