Any ability should never directly harm its user. Any twists from magic or external special abilities might, but otherwise no.
When it comes to using Unarmed in place of weapons, I would need to see the text but I imagine that it says "when using weapon X apply benefit Y [under Z conditions]" which would limit it to that weapon. I would need to know which sourcebook you are going from for this to be certain.
EDIT: I have done some browsing. The maneuvers themselves don't seem to require any specific weapons, but the feats that require the maneuvers do. So it all depends on what benefits the character wants to include.