In S05E2, after discovering that his men have started to behave out of Mike's control (such as executing hits on each other for money)
That is not completely accurate, as far as I remember.
After Gus Fring's death, Lydia Rodarte-Quayle, a former business associate of Gus, tries to convince Mike to eliminate all the loose ends (10-11 men) that could tie them (her) to the DEA investigation on Gus's meth empire.
Mike, a very cautious and rational man, flatly rejects Lydia's proposal and explains to her that those men were vetted by him and that he completely trusts them, also because they are financially taken care of. Killing them is not an option for Mike also because it might be drawing more attention and so it is an unnecessary risk.
Lydia, not at all convinced by Mike, decides to go behind his back and pays a hitman to get rid of everyone involved, but Mike, aware that something's off, manages to get rid of the hitman. Knowing that Lydia is behind the killing attempt, he decides to go after her.
But things have changed in the meantime. The DEA has found out about the offshore accounts set up by Gus and managed to freeze all the money, including Mike's which were destined to her beloved granddaughter.
Mike realizes that Lydia is still a precious asset because she can provide the methylamine needed by Walt and Jesse to produce the drug. He decides to spare her and keep her as a business partner in order to regain his money and provide for the necessities of "his" people in jail.
Sorry for the long preamble, but I guess it was necessary in order to understand Mike's choice. My guess is that his decision of "sticking" with "his men" is only partially based on his moral beliefs (do not betray your partners) also because in the show is never mentioned a particular bond between Mike and his men except for the business relationship.
I therefore think that his decision is based on a series of motivations:
- on Mike's confidence in his judgement (he picked those men, he interviewed them);
- on a careful balance between pros and cons of killing them (it's less riskier to pay them instead of getting rid of them);
- a sort of "honor code" between criminals that prevents Mike from betraying them