I won’t opine on other aspects of the two colleges, but on the CS curricula. In terms of CS requirements and offerings, Middlebury appears to be significantly better than Hamilton.
Hamilton CS professors helped establish a model computer science curriculum for liberal arts colleges and coauthored a textbook used nationally. Reputedly, the CS concentration is the most rigorous on Hamilton’s campus. I trust that the research-oriented direction Hamilton’s program has gone in has been intentional.
As perhaps an indicator of this, Hamilton grads earn the most in their early careers of any from the ten NESCAC LACs according to information in U.S. News. Although this represents a general figure, it might nonetheless be useful when comparing across colleges with similar curricula.