It's true that Ransom said that he did not choose his disciples, but the implication there is that they were sent to him - i.e. chosen for him by Maleldil's hand. That included MacPhee.
The inescapable fact is that not only was MacPhee listened to at St. Anne's, despite his skepticism, but his advice and requests were sometimes heeded. Remember how Jane was excluded from the councils, at least before Merlin's appearance, because MacPhee was concerned that listening to their discussions might influence her dreams? Even though he didn't believe that they were true clairvoyance (there being no room for such a thing in his worldview), he believed that something might be going on, and wanted to insure that something was unsullied by undue influences.
Of course, not everything he suggested was accepted or even taken seriously. Given the limitations of his philosophy, only certain avenues were open to his consideration - hence his talk of political parties and influence in Parliament, which is useless in the battle they're fighting. But this does not mean his advice is totally without merit. For instance, it is MacPhee whose knowledge of the natural order points the search parties to the right area in which to find Merlin - because he knows enough about terrain and groundwater to identify the only area in which Merlin's chamber could have been.
Another important thing to note is that MacPhee recognized the Director's authority. Tolerated though he was in the councils, when the rubber met the road and the parties were sent out to find the resuscitated Merlin, MacPhee was not allowed to go, and he respected that decision. Ransom was quite blunt about the reason, too: "You have never put yourself under the protection of Maleldil." (end of Ch 10) Interestingly, at that point Jane had not put herself under Maleldil's protection, either (that doesn't happen until the end of Chapter 14) - but at Ransom's pointed question, she puts herself under his protection. That's acceptable as a temporary measure. Could it have been that MacPhee's allegiance to Ransom was acceptable as an intermediary measure, until he could learn enough to acknowledge Maleldil's authority directly?
It's clear that MacPhee was modeled after one of Lewis' tutors, a Scottish rationalistic atheist named William T. Kirkpatrick whom Lewis nicknamed "The Great Knock". Skeptic though he was, Kirkpatrick was a rigorous thinker, and trained Lewis in logic and clear expression of his thought (something we all have benefited from.) Even as a Christian, Lewis acknowledged his deep debt to Kirkpatrick as a tutor and a friend. I think that in the character of MacPhee, and through him to honest and rigorous skeptics like Kirkpatrick, Lewis was commending those who made the best use they could of their rational faculties, seeking truth to the best of their abilities given their presuppositional limitations. MacPhee himself remains open to someday acknowledging God (see his goodbye to Ransom at the end of the book), but his honesty - or his perception of his own honesty - prevents him at the time.
One point I think Lewis was seeing with the character of MacPhee was that honest pursuit of the truth, even by someone who's limiting their means to materialism and empiricism, is more acceptable to God than the kind of dishonest spirituality expressed by someone like Straik. Though the crowd at Belbury talks the rationalist/materialist line, they don't really believe it. To them, it's a smoke screen to conceal their grasp for power. They have no compunction about cozying up to "the macrobes" the minute they deem it to their advantage to do so, despite the fact that the "macrobes" don't fit anywhere into the rationalist/materialist framework. (Though they're dead wrong about who is using whom.) If you want to see the spiritually foolish, look to Belbury, where their talk of scientific advancement and the pursuit of knowledge is nothing but window dressing on their pride and self-exultation. MacPhee is more the example of the noble pagan, seeking truth where he can find it. That will not save his soul, of course - only submission to Maleldil will do that - but it puts him in a much better position than even the "spiritual" in the Belbury crowd.