Intel?s Speed Step Technology implements this very task of lowering the clock frequency via software (ACPI). It does this by lowering the multi and voltage which subsequently lowers the clock frequency and current draw while in an idle state. It then returns to the original frequency when under any loaded situation. So as you can imagine the clock frequency will vary on frequent basis. More so than your situation
Its main purpose is to reduce power consumption to prolong the battery life of laptops. Intel also use this technology on desktop processor too (along with C1E support), mainly because corporate workstations are left on over night consuming and wasting electricity (so less consumption while idle is always a bonus).
C1E is similar in its purpose, but works via the OS sending halt commands (HLT) to the processor which reduces the clock frequency, and is akin to the processor throttling when reaching its temperature threshold.
So, I would assume it doesn?t have any dire impact.
Clock frequency has little impact on the degradation of the processor, and the same would apply for an alternating clock frequency as you suggest. Its heat and voltage which work against the processor?s integrity, but this is a pretty moot point in general.