I generally agree with Galastel answer: since you are already questioning, in your novel, the morality of your protagonist choices, you are reasonably safe from the trope.
Is all this enough to avoid the trap of making my protagonist seem like a saint relative to the antagonists, given that the antagonists are all irredeemably evil?
It's a good starting point, but it depends on how you do it.
Wetcircuit is stating this clearly in the comments to your question: having secondary characters chastise your protagonist is not enough, per-se.
In real life, if someone constantly acts against your morals or your ethics you'll eventually have to draw a line, or else you'll be acting unethically, too. If you think that stealing is bad, and your friend keeps stealing wallets from bystanders, there's a good chance you'll reconsider your friendship (either that or you'll be forced to lower your moral standards. Those are the options).
This happens for far less than immorality. It's not uncommon to cut bridges with people who acts like unappropriately, rudely, or just like douches.
Now, your secondary characters may realize that some of the protagonist actions are somewhat exscused by the current situation, his upbringing, or whatever else is the case. But here also, it's one of two cases:
- The relationship with the protagonist gets worse and enventually breaks
- The secondary characters begin questioning (and lowering) their own standards, condoning the protagonist actions, and eventually becoming as immoral as him
An in-between is possible: the secondary characters may still act like they have the moral high-ground, and yet the relationship with the protagonist stays unchanged. In this case, though, you ought to make clear that said characters are being hypocritical; maybe your deuteragonist (or better still, some other not-involved party) could point it out. I don't see this as a problem: humans can be bad, and humans can be hypocrites.
If I remember your previous question about Eldritch Abominations, it may be that the situation is so dire that your characters have to work together - wether they like each other or not. As you may have learnt from any workplace, working together is very different from liking (or even tolerating) each other, exspecially if there is something very valuable at stake.
It should be clear tho that you, as author and narrating voice, are not condoning anyone's actions. Present things as they are - murders are murders, and so on - and you should be fine.
Also, keep in mind that every thing I said should apply to your antagonists as well. So, no double standard there.
TL;DR: I don't think your protagonist will look like a saint. You seem to have already set up a story where morality is not a white vs black thing, but more of a scale of greys. However, there's always space for improvement on the grey-gradient.