No, makeovers are limited to profession-specific appearances. You can mix, for example on a mesmer, Prophecies mesmer face with Factions mesmer hair and Nightfall mesmer skin. But in your case, since Assassins are only available in Factions, you're limited to Factions Assassin looks.
The only use of the makeover to campaign-specific professions (assassin, ritualist, paragon, dervish) is to change gender (extreme makeover) or re-pick from the appearance choices that were originally available to them at character creation.
(When they first released the makeover kits, I was hoping we'd be able to mix profession looks, too. Was disappointed to find out it's not possible.)
Ninja'd! Blast my slow typing on this new layout!