While it is perfectly clear that a protracted siege would've left Julian's southern army vulnerable to the main Sassanid force, was he not capable of simply storming Ctesiphon? Its fortifications were hardly up to Roman standards, and razing the Persian capital to the ground once again would have been disastrous for them. Shapur would likely lose all his authority!
Storming the city couldn't have been difficult, since it was only protected by paighan - the cavalry was with the king. After that, the Romans would save their face even as the worst case scenario. The best case scenario would be the collapse of Sassanid authority, and thus a repeat of Trajan's conquests, and more.