Yeah, it took a bit too long, but not so long if you keep in mind originally his thoughts were restricted by two interlocked, negative factors: Kotori (her ability) was never a part of their plans or strategy, she was a hostile element due to Kana's prophesy. However, it's true that once Ryouta actually was with her, he should have realised her true worth as an ally (like all of us in the audience immediately did).
I'm happy Ryouta isn't totally clueless and indecisive. It was one thing to manage the drug factory robbery, but quite another to stop Neko by pressing the button. Furthermore, he even went to meet the annoying scientist with a decent plan and speech. Knowing the author I wouldn't be surprised if this scientist actually was a part of the organization handling these witches, though...