Why didn't Vito kill those two guys?

I don't think these two guys were made because made guys don't do that kind of collections with such small money.

Anyway, just like Walt and freeling10 said in the comment section, I think at the moment he was surprised as he invented a stupid excuse "It's a joke!".

Also he doesn't have his gun on him at this moment, so he couldn't instantly follow them and kill them in the parking lot for example. Just after this scene, at 42:58 on the episode, he goes home and take his gun in his bedside table then we can see him taking cash, then leaving on the run.

Another thing I thought, is these two guys are from Lupertazzi family (New York) and Vito is from New Jersey so he might know them, but he probably doesn't know where they live so he couldn't be able to track them home before the rumour spreads.

The knowledge of his bisexuality would spread so fast that he decided to flee instead.

I agree with Silver Bebs, but I will add a few more reasons, based on my observations.

Vito was visibly shocked to see them at 1:03 and after they left the gay bar, he stood there pondering. He didn't expect them to be making collections there such late. It's very likely he wouldn't be able to think straight after that encounter.

As to whether or not they were made guys, later when Tony was discussing this in the Bada Bing with the others, Carlo mentioned that Sal was "a friend of ours", which in Mafia lingo means made guy. Dunno about the other dude. Carlo emphasizes this fact so that Sal's words are to be respected and he's not just some associate mouthing off.

"Offing" some poor civilian schmuck in a remote rural area (like the guy whose car he crashed into and whom he shot in the back of the head, only because the guy insisted on calling the insurance company) is a lot different than hunting down two mafia associates in a big city - and mafia associates who could be expected to understand, after they caught him in a very compromising situation, that he might be dangerous. And anyway, even if he had attempted to follow / ambush them, by that time, the word (that he is gay) would probably already have been passed on to others.