Just played around trying to work out what you were saying, but now I get it. If a game is vertically orientated, even if it's played at 0° rotation inside MAME (ie horizontally) MaLa will respond by swapping into vertical mode.
So the enhancement you need is for MaLa to watch for the last-known video orientation from MAME rather than just (presumably) reading the relevant data on the ROM.
Have you tried the other option, which is to bind a button or a shifted button to rotate MaLa, and then MaLa causes MAME rotate to suit? This seemed to work better for me when I tried it a moment ago.
You're going to be telling something which orientation you want to play it in, so make it MaLa rather than MAME, since it works better for what you need to do this way. To stop playing Gyruss and start playing Centipede, you'd move your seat around to the trackball side, hit the MaLa rotate button so you can see what you're doing again, find Centipede and launch it.