I have no idea how RMU works, but in RM2 and RMSS, there are fundamental differences between the way martial arts and weapon skills are developed.
By default, martial arts require four separate skills to be developed to reach peak potential or, if using something like RMSS Martial Arts Companion, 1 - 2 attack skills plus a martial arts style. Conversely, being good with a weapon requires one skill. As such, doing what you're suggesting is going to have some potentially significant ramifications.
Having said all that, I don't think allowing martial arts skills be be included in the standard OB skill costs that can be allocated as you see fit is going to impact the game dramatically, unless you're also using some of the optional rules with players that are actively seeking to break the system (I'm thinking at least one way to demonstrate possible flaws with this rule would probably involve starting with a High Warrior Monk).
The inherent balancing factor, however, is that you're still limited to two ranks per level, even if your primary weapon cost is 1/2, and a non-monk character moving a weapon cost to martial arts still isn't going to be as good at martial arts as a warrior monk.
Personally, I don't really see anything to be gained by such a house rule, but I don't think it's likely to cause any major headaches.