Atlan had to think fast. He lost his only protection, which meant that he would have to bear the full brunt of the Canzer's force.
He could choose to simply let himself be trampled since his battle suit armor allowed him to withstand 5 full-powered attacks from Canzers.
However, he knew that even with its shy nature, the Canzer tended to be vindictive. The Scout was subjected to multiple tramplings just because he was a human who dared to touch the Canzer. Who's to say that it would be so magnanimous as to finish stomping Atlan with just five steps? Maybe it wouldn't stop until ten or twenty.
Sure, he had 5000 years of SoulTime in his System to help him mitigate the damage, but that was his lifeline—literally. It would be ideal if he didn't spend so much of his SoulTime on the first Canzer he encountered in this mission.
Therefore, he couldn't do nothing. He had to get away by himself.