I think they could, but it's not as simple as Flowey simply not having done anything evil...
Because even if you don't take Sans' "you'd be dead where you stand" threat seriously, after a few neutral runs Flowey will warn you not to tell Sans anything about you. This implies that if not for his promise to Toriel, Sans really might have followed through on that threat after all.
This is because, presumably, Sans' reports about the timeline exist regardless of whether you go through a murder run. those tell him that a being with the power to control time will destroy the world. The only solution he can see to this is to try to destroy it first--kill, or be killed. So when Flowey shows up, and reveals he has the power to reset, well, he's a threat regardless of his actions. As far as Sans can tell, this is the creature that will end everything eventually.
I think it's toriel's promise that makes Sans rethink this very grim, pessimistic outlook on the possibilities, and that's what I went with in Unexpected Guests. Sans isn't inherently eager to kill or fight, but he'd trapped himself into thinking it was the only option. Talking to toriel, listening to and getting to know her, got him thinking and ultimately gave him an out. He's still pessimistic about the chances of the timeline coming to an end--but he's willing to give Frisk a chance to prove that pessimism wrong, and really, he'd much rather make friends.
With all that in mind! When Flowey controlled the timeline, as long as he didn't tell Sans about his power to reset, they could be friends--Flowey himself says he befriended everyone in canon. I bet they pulled all kinds of pranks on people, and at times when they felt more contemplative, Flowey might ask Sans questions about time travel or philosophy and such. I don't think it'd be quite like Flowey's friendship with Papyrus because the brothers are different people, and I do think flowey would get as annoyed with sans' puns as papyrus does XD but, they could almost certainly find some common ground and not by just standing on the same patch of dirt
But Sans would have reason to be wary of Flowey no matter how nice he'd been so far... <:/
At least, that's what I think is going on ^^;