I'm not sure whether you mean officially (legally) or in terms of public image, but I will answer for the first. Constitutionally, the president has very little control over members of Congress. He does not appoint them and he has no ability to punish them or try them, that authority resides in the Congress itself. Even if Eisenhower had more control than he did, McCarthy could still reasonably claim protection on first amendment grounds. There is very little that he could do. The most effective means possible for Eisenhower to stop McCarthy would have been for the president to ask the party leadership to punish McCarthy, but even that would be difficult. It requires the cooperation of the leadership (which is harder to get than you might imagine) and they still cannot make an individual senator do something; US senators can be some of the most independent politicians in the world if they want to because of the way they are elected and party structure.

tl;dr Eisenhower had almost no means of forcing McCarthy to do anything in terms of political or legal means. Whether he might have put more public pressure on McCarthy to stop is a different question that I am not qualified to answer.