The transmission is not "glass" and if you are worried about it retrofit the clutch delay valve later WRX's have as subaru's real fix to the "weak" transmissions. They made it impossible to drop the clutch which reduced the shockload on the transmission. Or, don't drive like an idiot and it will hold up fine.
RWD conversion can be done with the transmission still in the car, but it will make the transmission weaker, not stronger. All your power will be going through the rear transfer gears and the r160 rear diff, both of which are not strong enough to put up with much abuse. I've grenaded multiple r160's with a 135hp 2.2l. Shredded a few sets of rear transfer gears too.
You're taking all the power and running it through gears only designed to handle half the power. That's increasing stress, not reducing it. RWD will also encourage abuse.