Possibly, but I'd give it to the Heroes more often than not. You've got: Hiro who's space and time manipulation powers would be a royal ****ery to contend against (Peter would have those as well if you count his alternate incarnation, and Hiro's future incarnation has developed these powers at a pretty extreme rate), Illusions from Candice (and Sylar of you count his alternate incarnation), Maury's Psionic abilities, Nathan who can fly and who's exceptionally fast in his own right anyways (Sylar can do the same if you count his alternate incarnation), Eden's powers of persuasion, the Hatian's large scale memory effect powers (he was able to wipe the minds of his entire village at once, pretty large scale) as well as Ted's (+ Peter and Sylar's) radiation ability, which can be pretty large scale; would be good plan B attack.
Plus, given that these Heroes abilities are "alien" to the Smallville Universe, Clarky would be vulnerable.
Yet, the only incarnation of Peter that has been shown to bend the time-space continuum at will is the Dark Future Peter. Whether his current incarnation was able to so in an uncontrolled way or not is absolutely useless in this scenario. An uncontrolled or instinctive usage of an ability in no way guarantees a replication of such an usage in a completely unrelated scenario. In respect to the scenario and circumstances at hand, the only Peter that would be able to properly utilise the mentioned powers is his future incarnation.
how about Heroes Crossover with Crysis game series(where Emile Danko uses Nanosuit Technology to levels Playing fields between ordinary humans and evolved humans, and forget about Nanosuit being symbiote thing)?