It depends on what how old Turing was... if it's 20 year old Turing -- an electron microscope wasn't invented yet... so no, he couldn't use one to see all of the structures of a CPU.. just the larger structures visible with an optical microscope (limited to ~200nm (Rayleigh criteron) but I dont know if they had the lens manufacturing good enough back then to reach that limit)... which may not be enough for him to figure it out.
Edit: And even when he died in the 1954, electron microscopes werent that advanced... we still needed to invent new techniques, improve our lens manufacturing, etc. There were a lot of shortcomings with it back then that limited its usage. So even in his later years, I wonder how much detail he could actually see on a modern CPU.
Of course he could, but unless you told him you were a time traveler from the future, or the Germans had vastly superior secret technology they hadn't deployed yet, it would be so unlike the computers of his time that it probably wouldn't seem plausible that it was what he knew of as a computer.
Edit: And even when he died in the 1954, electron microscopes werent that advanced... we still needed to invent new techniques, improve our lens manufacturing, etc. There were a lot of shortcomings with it back then that limited its usage. So even in his later years, I wonder how much detail he could actually see on a modern CPU.