In case you forgot, Sylar was not affected by freezing time.
He was - Time resumed before Sylar grabbed the sword. Notice that his mother had been frozen in place as she fell. Time resumed as hiro swung the sword and she continued to fall to the floor.
IIRC (I'll have to go back and watch to double-check), I seem to recall that there was a painting showing the cheerleader on the steps with "Sylar" looking down on her, but when it came to that point in time, it was Peter in that actual position. I swear I remember pointing this out to my wife.
There were 2 separate paintings. 1 of peter lying dead or dying in front of the clock - this was the initially missing panel. the other was a cheerleader [thought to be claire] lying dead with sylar standing over her - it was the painting that peter finished via tapping into isaac's ability.
Is this what you meant or something else?
The future can be changed. Even Isaac told Sylar they will stop him. I doubt he was referring to the "future" that Hiro just came back from. Otherwise, why not just let things run their course?