Yes, if it did before you cast the spell
As a general rule, spells only do what they say they do and no more, so whether or not the animal considers you or your allies hostile is unaffected by the spell. (Source)
For example, let's us consider a case where you cast this on a wolf so you can get inside its lair where the ancient plot mcguffin is buried. Ignoring the spell, the GM might decide the players can either fight the wolf, or make a persuasion or intimidation check to get past it if they act accordingly.
If you approach the wolf threateningly, and possibly even start a fight before casting the charm spell then yes, the wolf will continue to consider your allies hostile, they just can't attack you and you get advantage on social interaction checks with them. The GM could also rule that you're at a disadvantage on this check now if you've hurt the wolf, so the advantage from the spell would cancel out leaving you at a normal roll.
If you instead approach alone and cautiously, cast the spell at the earliest opportunity and try to calm the wolf (persuasion) or scare it out of the way (intimidation) you'd be at advantage on the roll, and will find it much easier to get past the creature.