My personal feeling is that psionics is different from magic has too bad effects: first, it removes the essence-channeling-mentalism triad that helps the feel of psionic stuff in fantasy (for me, anyway). Second, unless you have about a 50-50 split between the two forces in the world, you're going to be giving a power boost to whichever is the minority. A bit too much of a boost to my mind. The reduction by 10 (as recommended) of SR or its complete removal would have a drastic effect on the difficulty of foes the group will probably start seeing long about 6th or 8th level.
Not to mention that if it's different, arcane/divine dispel magic won't work on the psychic warrior, nor will a globe of invulnerability or other anti-magic effects. Way too dangerous.