A few problems:
1. While Arago could grab Mercer with Claw, it wouldn't do much to restrain him. Alex Mercer has shapeshifting, body control, and an amorphous body—unless Claw has some kind of paralyzing effect, he can probably squeeze out of it. Besides, restraining him wouldn't limit him from using ranged attacks, while bringing him closer is a really bad idea.
2. Whether "Alex Mercer" (or rather, the former Alex Mercer's reanimated body) has a soul (or possibly even multiple souls) or not is questionable at best. Personally, I find it unlikely that "Alex Mercer" still has a soul, since he's basically a corpse reanimated by a virus, and the original Alex Mercer was clinically dead before being "revived" by the virus. Generally speaking, neither viruses nor reanimated corpses are thought to have souls.
3. Even if prolonged contact with Arago can cause decay due to overflowing life energy, Alex Mercer has the regenerative ability to overcome that. Additionally, Mercer has shown an impressive ability to absorb large quantities of biomass—which is merely the physical form of "life energy" (E = mc^2, after all)—which could possibly mean that Mercer would be able to handle a far larger amount of life energy from Arago without suffering ill effects than would normally be possible (hell, it might even make him momentarily stronger). Plus, there's the fact that prolonged contact with Alex Mercer is equally dangerous, since he has the tendency to absorb people whole (sometimes in pieces).