I was unable to access the console (perhaps because I use a Japanese keyboard).
If you're unable to access the console, you can add the [seta in_mouse "-1"] (without brackets) directly into the game configuration.
Go to the c drive for the bottle where you've installed MoHAA. Go to:
Program Files/EA GAMES/MOHAA/Mainta/configs
Program Files/EA GAMES/MOHAA/Maintt/configs
and open unnamedsolder.cfg with textedit.
Add [seta in_mouse "-1"] (again, without brackets) to the end of the list, right after the other seta commands. At the end of the list you'll see
//
//Aliases
//
I put it right before that. Like this:
seta in_mouse "-1"
//
//Aliases
//
That solved the mouse problem for me.
There are two different folder [mainta] and [maintt] and one is for Breakthrough and the other is for Spearhead, but I don't honestly know which is which, and I suppose it doesn't really matter since they both have the same problem and can both be solved by Paul the Tall's excellent tip.