I don't know if the MT windows are considered raid frames or not, but you could set up a healing macro that will let you heal using either a Flash or Greater heal (depending on what you cast) based on mouseover the frame and hitting the macro key.
For my paladin, I use the following macros for healing and cleansing, that seem to work remarkably well for things like this:
Cleanse (Decurse)
/cast [modifier:ctrl,target=player] Cleanse; [target=mouseover, help] Cleanse; [target=target, help] Cleanse; [target=targettarget, help] Cleanse; [target=player] Cleanse
Flash of Light (Max Rank)
/cast [modifier:ctrl,target=player] Flash of Light; [target=mouseover, help] Flash of Light; [target=target, help] Flash of Light; [target=targettarget, help] Flash of Light; [target=player] Flash of Light
Holy Light (Max Rank)
/cast [modifier:ctrl,target=player] Holy Light; [target=mouseover, help] Holy Light; [target=target, help] Holy Light; [target=targettarget, help] Holy Light; [target=player] Holy Light
Just substitute for priest healing and cleansing spells and you're all set.
Now, if the MT frame doesn't work like a raid frame, then.... sucks.
