That's a good point - it wasn't until issue 14 of the Silver Age issues (over 2 years into it's existence) that the "anti-mutant hysteria" plot was really hit upon. It's a milestone issue (rather gloriously it mentions that the title is going monthly from #15 due to "unprecedented demand" which is... wishful thinking).
Kirby only did three more issues, and Lee five before Werner Roth and then Roy Thomas (first, less successful run) took over and they didn't focus on the anti-mutant aspect.