Altera would be interesting case... I mean, she can't beat Gil, at least without Master's support but she could have beat him if she turned into Sefar, but that's only Moon Altera.
Earth Altera meanwhile can't do it simply due to how Moon Timeline and Earth Timeline go (aka Sefar's real body not going to the Moon Cell in the latter due to it not existng). I mean she is still strong, matching Iskandar in Fate/EXTELLA (I mean it's Moon Altera, she beat him in their first fight but only due to the former not being used to the Moon Cell but in rematch, they were not only seemingly equal and had a draw. I could probably try to use Fate/EXTELLA Link info too... if I had played that game fully which I didn't. Anyway back to Earth one since we are focused about her and not sure if Moon could scale Earth Altera which is probably no.)
As for if Kiritsugu had any conflict with Altera. Well, it says that, quote:
"She treats her Master stoically, recognizing them as a general or adviser-like figure, and will generally go along with anything they say with an “I see”. Instead of trusting as a human being, the situation is closer to a fighting machine on the battlefield that fully relies on external software (the Master) to process thoughts."
So she would probably be okay with him. And if needing to destroy the grail, she wouldn't mind it either, despite having a wish.
Probably only issue would be Gilgamesh being in the war but there may be a chance they could beat him if Gil decides to go a bit soft (which he will probably don't) but you know what else he could do? Maybe use the favor Gil has with Altera/Sefar for sparing Gil's father since with it, that's how Gil joined Altera faction in EXTELLA. I mean it may probably don't work since Gil only kinda truly joined to make sure Hakuno was safe but still.
If that will not work, then I guess they must pray that maybe Altera can use Teardrop Photon Ray (but it will probably not work but eh, they can try).