Ok, so from the first time we meet him, the Haitian (do we know his name?) was assumed to be a villian, working with Bennet and the Company. However, I believe this reaches a turning point when he does not take Claire's memory even though he is sent to do so. A while after this point, it seems that Claire can confide in him behind her "father's" back. (Ally?)

Then, we see him work with Bennet to protect Claire (shoot him, take his memory), although he winds up handing her straight to Nathan and Angela Petrelli. (Enemy?)

Now, we have been introduced to him in Volume Two as having been afflicted with the same virus that Molly and Shanti (Mohinder's sister) had before. Then, he takes Mohinder's memory of even having met him. (?)

Now we know that he's working with Bennet again, but we also "know" that Bennet is working with Suresh to destroy the Company. Does this mean that he has switched sides and is no longer actually working for the Company, as are Bennet and Suresh (or trying to take it down from inside)? If so then why would he have needed to take Mohinder's memory after meeting him?

Actually, he did not take Mohinder's memory. It was just a sham to fool Bob. For further details read the Graphic Novels on NBC.com. There's one that shows what happened in the conversation between Mohinder and the Haitian. Mohinder tells Haitian how to find Bennet, and tells Haitian that he will pretend to have been memory wiped. Haitian then leaves to consult his dead father (do some ritual thingy)...

Wow! That's pretty cool. Guess I should have done my homework on that one... Thanks!

i think he is more of an ally to HRG, Mohinder and the good heroes and is an enemy to the company
as HRG, Haitian, Mohinder, Matt are all in a team to take down the company