Probably won't happen but if Hiro decide to teleport him and Charlie into the time Hiro came from then Charlie would disappear since she wouldn't exist in the past.

Nah, I don't think Heroes' time travel works that way. And logically speaking, the only way Charlie could disappear is if it was the Charlie from the present time line... And the current Charlie is, well, a corpse. So there'd just not be a grave somewhere anymore.

Because of the butterfly effect, this would completely alter the entire storyline of the show. I think it's pretty clear that Hiro will wind up not actually going through with this.

Heroes time trave definitely allows messing with the past and influence of the future.

It would be interesting to see how they would handle the "butterfly effect" of that, since it would potentially disrupt Sylar back in S1, and at least deprive him of one usefull ability. Not perhaps his most powerfull ability, like TK, but it would still have some impact. Would everything be better, or will Hiro bring her back only to find the world in total chaos and then come to the painful decision that he has to take her back to die?

Those two years in-between seasons would vanish for her. She'd have no memory and be 2 years younger then she is. There is no reason to think that you must replace yourself in the time you go to. Peter and Hiro have both been to times when there have been 2 of them. If Hiro is not careful there will be 3 of him in some times.

Hiro could have gone back in time instantly and stopped Samuel from taking Charlie a second before he did.

Sure, it would have been easier, but would it have made for more interesting television? Probably not.

this thought really excites me because if they choose to they could have an army of heros to go against one seemingly unbeatable enemy(maybe a series fanaily against villian not met yet)

In real life if there 's such thing as super powers, Hiro would go time travel to before Samuel snatched Charlie and maybe put Sammy in dino world. It wouldn't affect Hiro's past life if Samuel is dead.