Sylar had already been overwritten--it's just that the "Nathan" program was incomplete. Since Sylar already had Nathan's memories by that point, selectively wiping Sylar's memories (which the Haitian can do) would leave all of Nathan's memories and enough of Sylar's for his shape-shifting power to still work. Either way, having Matt help would have been preferable, but the Haitian should have been a viable fall back plan if Matt kept refusing to cooperate.