Tom's decision to abandon the stones of the first floor was fully rational. While there was no limit to how many stones he wanted to bring home, there was a hard limit to how far they could go with just their firearms alone. As such, there was a pressing need for both Tom and Claudia to get stronger, something that could only be done with the help of said stones.
But there was a major problem occurring whenever stones came into play. While the fact that neither Tom nor Claudia knew exactly how to make them give up its energy for the sake of improving their bodies was a major problem, it wasn't something that would prompt Tom to such a rash decision.
It was all about time.