Yes, Thanos destroyed half of all life, but that's only because it was allowed in the TVA's Sacred Timeline. If Kang didn't want Thanos to carry out his plot, he could've easily stopped it. After all, the TVA is filled with useless Infinity Stones, reducing the items that gave Thanos his power to mere paperweights.

Is the TVA stronger than Thanos?

Marvel's God of Mischief took this to mean that the TVA is one of the most powerful forces in existence (more powerful than Thanos or the stones he collected).

Can TVA capture Thanos?

Now we know that the TVA could go to any timeline and could apprehend anyone. So yes, probably capturing Thanos could've been a little more complicated than Loki, but they could've done it.