Hmm... I think the X52 Pro ministick on the throttle default maps to mouse inputs so I don't think you can get around it ingame, unless you also map your mouse commands to Shkval slewing which will have lots of unintended effects.
I, too, have an X52 Pro and could not find a way around not using the Saitek profile tool, but it works great for me. At a minimum you can create a profile where you "unmap" the ministick axes so you can map them ingame.
[edit: I don't know about yours, but the ministick on my X52 Pro has a lot of noise on it, which may make it unsuitable for use as an axis controller]
Edited by EinsteinEP (01/30/12 04:36 PM)