I did a very exciting battle with a Kraken in D&D 4e. Like you, I realised that the players would try to attack the tentacles. But I also realised the Kraken entry in the Monster Manual is kinda bad.
So instead I designed a custom monster. In addition to leeching some powers off the original Kraken, I gave it a "raise tentacles" power that would summon a number of Tentacle minion creatures. Hitting one would "kill" it, causing the Kraken to pull it back and dealing it 5 damage. The Tentacle minions would take up 2 spaces and have no Reach, but they would move around a bit.
This helped me get around the limitation you mentioned and made the battle much more exciting and lively, as the Kraken would slowly withdraw arms and then occasionally spend an action to bring most of them back into the fray. Felt much more like a giant squid trying to crush a ship.
(I also made the beast rise up at the end of the ship and bite at things, so the players could also attack its head if they felt like it, with the risk of being shoved into the thing's mouth)
If you don't want to go the long way or need a quick option for other situations where a large beast with Reach swings out with a large appendage; I allow players to ready an attack on the creature when it swings out, and a player who is grabbed is allowed to make attacks against the creature as long as the grab rules allow it. But I don't trigger "enters the square" effects for them, as it's only a small part of them moving. It doesn't seem to cause any major balance issues. Most people don't really want to be grabbed or mauled by things so big they have that kind of Reach, so they make other plans to deal with them.
The pathfinder SRD says:
Temporary Bonuses: Temporary increases to your Constitution score give you a bonus on your Fortitude saving throws. In addition, multiply your total Hit Dice by this bonus and add that amount to your current and total hit points. When the bonus ends, remove this total from your current and total hit points.
Example:
Let's say you have a lv 5 character with a total of 30 hit points. If he would receive a Bear's Endurance spell, he would gain 10 hit points (Con modifier increases by +2, 2 times lv = 10).
Note that these are actual hit points, not temporary hit points. This means these hit points can be healed back like any other hit points gained through Constitution.
Let's say you take 15 damage while under the effect of the spell and drop down to 25 hp. When Bear's Endurance expires you would lose the the previous 10 gained hit points and drop down to 15 hit points.
To sum it up: When max HP increases by x, your current health increases by x. When your max HP lowers by x, your current HP lowers by x.
Best Answer
I tried the same thing you proposed, and it shortened combats and made things more interesting. I think the combats in DnD-4e are too long and can become boring so anything that make them more interesting is welcome.
But it depend on the group of players, one group might like it and another might not. One group once said that you can't die in DnD-4e, so I halved the HP and they were happy. The other group wasn't happy with halved HP so I introduced mini skill challenges in combats where it existed an alternative solution and they resolved a lot of combats by passing skill challenges mixed with combat, and they were happy too.