If I understand your example, the PI of a project was also on the ethics committee and disagrees with the recommendation of the majority of the committee. If this is what you are actually describing, the member of the committee who is also a PI of a research project seeking ethics approval must recuse her or himself from the decision of the committee.
A bit more since I had a difficult time understanding your example - if you just mean a researcher who is proceeding to carry out research despite an ethics committee refusing to approve a research proposal, there should be an appeal process if a researcher disputes a recommendation from ethics committee but the resarcher cannot just proceed to carry out research since he does not agree with the recommendation of the committee. Further, to proceed to carry out research that must have ethics approval if it has not been approved should lead to an investigation of the behaviour of the researcher under the university procedures for displinary investigations.
If the head of a project refuses to comply to the decision of an ethics committee, I think it is required you make a formal complaint to the ethics committee about that. Not to do so will make one liable to the same crime.
You have perfectly understood the problem. The PI of a project was also on the EC and disagrees with the recommendation. I completely agree with you that PI of a research project seeking ethics approval must recuse himself from the decision of the committee. I wrote a letter to the Ethics Committee asking them to exclude PI from decision making process. I only wanted to know that I did not make a mistake in something and whether there is an international EC that would like to resolve this issue if it is not resolved in the right way.