I think you've got it right there! There is only 1 timeline, Sylar survives by stealing DL's power and Peter explodes. Nathan blames Sylar to save his brother, Peter falls out with him over it and leaves.
Hiro then has a lot to do, he realizes that he has to travel forwards and backwards in time manipulating things to make sure Peter is strong enough to defeat Sylar at the end of the last episode (just after he dies). He tells Peter to save the cheerleader and is in the background all the time tweaking things to make sure that the correct path is followed and Sylar is defeated.
TBH thats just the storyline i'd like to see. It would fit and we could see Hiro popping up at random moments in other series'! Would be great, for example, to see him stop Peter and Nathan's dad from getting hit by a bus