If (and that's a big if) Vali gets his way, then yes, the MC's harem won't matter. Given the way Vali's been talking, though, having a harem is more about which girls are useful to him, than sexual interest. It just doesn't seem to actually matter much to him outside of usefulness, and he pretty clearly has no interest whatsoever in some of the girls, like Glasha and Kimmy. He likely considers the current harem pursuit to be a useful distraction to keep the MC from thinking about the ramifications of their mysterious 'deal'. As for Vali's old harem, almost all of them are pretty clearly long-dead (Natasha is the only one of his lovers we know is still 'alive', and while he was a bit annoyed at the MC flirting with her, he didn't seem to care that much about it even with her reciprocating a little), so he'd be starting a new one based on who was useful to him, perhaps with the intent of stealing some of the MC's girls by pretending to be him, if they don't know about Vali.
Besides that, what else can the MC really do? Vali's inside him already, so he can't really go back on the deal without knowing what the deal actually was in the first place. So his choices are to resist and have Vali fuck him up constantly and screw up his life, or he pretends to go along with Vali unti lhe understands enough about magic and/or their deal to extract Vali safely, perhaps with Liliah's help (which seems to be the route he's taking). It's possible that decision will be reflected later in the reluctantpath vs eagerpath variable choice.
That said, I am firmly confident that Vali is not intended to 'win' on the harem path. IMO, Vali is being set up as an antagonist temporarily allied with the MC for his own purposes, not as an ally. Blackhand has also made comments about allying with various factions in the future, so it's always possible a poor decision in of those faction choices could lead to a Vali-controlled MC and a Bad End.
