1) Kiritsugu couldn't harm Kayneth because the contract said that only
Kiritsugu couldn't harm him.
2) Maya, on the other hand, wasn't mentioned anywhere on the contract and therefore can act freely.
3) Maya kills Kayneth and company on orders from Kiritsugu.
So, in summary, Kiritsugu never violated the contract.
At least, that's my interpretation of what happened.
