Personally, I'm opposed the Hirogen being a faction such as this.
I want my Hirogen as part of the Romulan thing...blah, blah, blah - I've mentioned that a few times.
On the other hand, a non-aligned faction - presents some interesting gameplay potential. A mercenary type of play... where you fight for or against the various factions - whether in PvE or PvP. You could select Faction A for a particular arc, but maybe Faction B for another...etc.
One could even imagine actual "Reputation" - where your doing things for Faction A means that Faction B may not offer you things to do - may even reach the point Faction B will not speak to you outright and you'll have to find a way to get back on their good side if you want to do something for them.
Etc, etc, etc... yes, it's not core Star Trek in the least - but the Universe is vast and we saw plenty of mercenary type characters.