A couple things:

1) Intel is very heavily invested in x86, and they're likely to be very reluctant to change.

2) The Mill folks have patents, which might be hard to work around.

3) If the Mill becomes successful, they're likely to either be bought out by one of Intel's behomoth competitors, like Samsung or Qualcomm, or perhaps even by Intel itself.

4) If Intel really likes their technology, they could license it from Mill Computing. It would be surprising for Mill to say no to a reasonable offer, considering that they don't have their own fabs and it's their business model is to license their designs to those that do.