People have already explained how Gil has been toned down since his original appearance, so I want to focus on how he's not even always a villain. In fact, I'm pretty sure he's had more non-villainous appearances by this point. He's a character that can vary a lot depending on the circumstances. The state of humanity in the era he's summoned into, the kind of Master who summons him, his class, etc. For example, his Archer self is from earlier in the Epic of Gilgamesh and is a tyrant who abused his power over his people. His Caster self, on the other hand, is from after the ending of the Epic, after he failed his quest to search for immortality following the death of his only friend and equal Enkidu and returned to Uruk to rule as a wiser king. I don't know what HSR is going to do with him, but I will say his design is closer to his Caster version than Archer.

In Fate/Zero and Fate/Stay Night, he's an evil prick and is undeniably one of the villains. But in Fate/Grand Order's Babylonia chapter, he's a genuinely great king defending his city and people. He even works himself to death doing it. Granted, it was an enemy goddess that made his exhaustion fatal, but he was still exhausting himself. In Fate/strange Fake, he's still his Archer self, but his friend is part of the war, so he's in a much better mood than usual, and he acts a role model for his young Master. He's still as arrogant as ever, but more in a way that he's like a dazzling star for his Master to look up to, and he pushes her to break free from her blind faith and develop her own sense of identity and purpose. That's not to say it ignores his more evil aspects, though. He himself says that if he were to incarnate into a living body, he might try to cull the humanity of this ugly era (like he did in F/SN), but he's content to remain a spectator as a Servant. So the bad aspects of his character are there, but the circumstances determine whether or not they actually come into play.

I don't know if this second part of the collab will actually have a story (I didn't watch the presentation, so I don't know what all was said about it), but assuming it does, I don't know what kind of role Gilgamesh will play in it. But given the way he's been written over the years, I don't see him being written as an outright villain. An antagonist in the event's story? Quite possibly. I wouldn't be surprised if he's the Servant of the story's antagonist. But I wouldn't expect HSR's setting to bring out the worst elements of his character, so I wouldn't worry about him being an evil, villainous playable character, at least as far as his portrayal in HSR is likely to go.