I think you're right by RAW; elves' Fey Ancestry and bards' Countercharm only grant advantage on saving throws against being charmed, and therefore can't prevent something inevitable like this. There are a number of spells in the same boat, such as Aura of Purity.

Of course, there's a flip answer of "don't become incapacitated" and "don't let the warlock touch you". The rules are full of ways to do that, although some of them are complicated and most of them are fallible in one way or another. But, let's say that those things are unavoidable...

Prevention

Spells:

• Protection from Evil and Good (1st level cleric, paladin, warlock, and wizard spell) possibly could work, although it only prevents being charmed by aberrations, celestials, elementals, fey, fiends, and undead.
• Magic Circle (3rd level cleric, warlock, and wizard spell) is the same, but curiously leaves out aberrations.
• Hallow (5th level cleric spell) Has the same caveat. This has a 24-hour casting time and consumes 1000gp, but has a duration of "until dispelled", so if you know you're going to be fighting a thrall-creating warlock outsider, this might be a way to prepare.
• Contingency (6th level wizard spell) plus one of the cure spells of 5th level or lower (presumably Remove Curse, since that's the one available to wizards). This isn't quite prevention, since it can't keep the effect from taking hold for an instant before being removed, but I'm going to count it as such, because while it probably feels unpleasant, being charmed isn't that bad when no one has any time for actions.
• Antimagic Field (8th level, cleric and wizard spell) prevents magical charms from affecting targets in the sphere; presumably the "alien magic of your patron" is also temporarily suppressed when thralls are in the field, unless the patron counts as an "artifact or deity".
• Mind Blank (8th level bard and wizard spell) This is probably the winner. Lasts 24 hours (not concentration; whew!) and grants immunity to the charmed condition. It's 8th level, though, so the Create Thrall ability becomes available to players one level earlier.
• Wish (9th level sorcerer and wizard spell) One of the standard effects is immunity to a specific magical effect for 8 hours for up to 10 creatures; you could chose this one. But using Wish in this way risks adverse effects including possibly being unable to ever cast Wish again. If you just need to protect one creature and have access to Wish but not Mind Blank, using Wish to replicate the effect of that spell would be a better option.

Other:

Don't be humanoid. The effect specifically targets humanoids. As I read the rules for effects like Wild Shape and similar, it appears that these make you no longer humanoid, but it also does not seem to be spelled out exactly in the rules we have now. The effects do tend to say "the target's game statistics [...] are replaced by the statistics of the chosen [form]" — but it's kind of nebulous to me whether "creature type" is a game statistic in 5e, or whether affected creatures are "humanoids in beast form" for the purposes of this spell, or truly "beasts". In any case, the 8th-level spell Animal Shapes specifically says that it "turns others into beasts"; if making a DM judgment call, one might separate out the spells that preserve mental ability scores from those like Polymorph, which do not.

Be a high-level berserker. At 6th level, the Path of the Berserker barbarian gets Mindless Rage, which prevents being charmed while raging. A rage ends if the barbarian doesn't keep attacking (or taking damage), which is likely to happen if you're incapacitated. But the 15th level Persistent Rage removes that limitation, so as long as you stay conscious, you're safe — at least, until the 1 minute limit.

Cures

• Monk's Stillness of Mind, which can end a charm effect as an action
• Remove Curse (3rd level cleric, paladin, warlock, and wizard spell) by the ability's own description, of course.
• Dispel Evil and Good (5th level cleric and paladin spell) can end charms with a touch
• Greater Restoration (5th level bard, cleric and druid spell) ditto
• Hallow can also end the charm effect, with the same "outsider" caveat under "Prevention"
• Power Word Heal (9th level bard spell)
• Wish (by emulating Remove Curse)

Yes, cloning, repeatedly, maintained, could make you immortal.

There's some logistical concerns that make this trickier than the spell itself:

Vessel must be undisturbed

So, ideally, you set up a nice young version of yourself, hide it away for the time something goes wrong and go about your life, right? Well, the longer it's around, the more likely, over time, something COULD happen to it. Especially in a world where you've got things like purple worms, umber hulks and bulettes and other critters that dig through granite like butter.

Well, then it makes sense to set up some defensive measures, right? Traps, spells, etc. But in the world of D&D, the more defensive measures you put up, the more people assume it's got something valuable to steal...

Now, as a GM I wouldn't just automatically assume something is going to happen, but if the clone is sitting around for decades, or the wizard in question has enemies seeking them out, then we'd start having to think about problems.

A giant diamond

So, the diamond is worth 1,000 gp. This doesn't mean you can simply pull out 1,000 gp and find these diamonds anywhere, everywhere. There's got to be a limited number of them. You're probably not the only caster who is looking into this spell.

So, a bunch of wizards want immortality from a limited resource and are all looking for it.

I'm sure that's not going to lead to problems.

Welcome to the Immortal Club

So, if you manage to live far beyond even what most D&D world folks know people to be capable of, and you're known to be an awesome wizard... how many other people are going to be trying to get your secret of immortality from you?

How do other things which are immortal feel about this? Do they find a way to manipulate/play you because you're new to this game? Do they already have a control on the 1,000 gp diamonds and dole them out to the few wizards who have Clone just to keep them under their leash?

Is there an alliance of lichs who are jealous you've found a way to live, but actually live, not undead live, and they'd like to simply stomp you down for being audacious?

Are there mind flayers looking to eat the juicy mind of a super-intelligent wizard with 800 years of tasty-tasty knowledge?

Are there divine guardians of life and death who did their accounting and finding there's a soul short that needs to move on?

Gameplay

Unless you're playing a very unusual game of D&D, these issues aren't likely to come up too much simply because the timescale is too short. But it makes excellent source of adventures based on NPCs - just imagine what happens when you do have a wizard who has been doing this and dealing with all of these problems and what that means for the PCs when they get involved in it.