I heard that a skill respec on your character can allow you to change reputation abilities, but I haven't seen it said definitively anywhere so that's a bit much to risk (and very expensive) just to change one reputation ability choice.
The respec thing works, I respec'ed one of my toon once for a brand new breen ship build and I head in infected and noticed none of my rep passives were working (was tier 4 at the time). I was pleasantly surprised when I checked the rep status, I noticed I could choose all over again the entire rep skill tree. So I am confirming that the entire rep passives are reset giving you a chance to set them all up again at the cost of a respec token (both for romulan and omega rep). Not bad imho.
**~Reality under scrutiny~**
Fed Fleet: Operation Omega Task Force | KDF Fleet: KHG Klingon Honor Guard