How to differentiate between a list and parallelism

In the case of a list of only two items, it is better to rephrase the sentence (as already done in the case of one meaning in the question) than to rely solely on punctuation.

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Without more extensive rewording, a common way of distinguishing the two is to use numbers in parentheses:

1. I want to discuss the inhibition of (1) reflexes and (2) skeletal relaxation.
2. I want to discuss (1) the inhibition of reflexes and (2) skeletal relaxation.

But if you are speaking strictly of punctuation, only one of the meanings can be made explicit—and it uses a nonstandard construction:

2. I want to discuss the inhibition of reflexes; and skeletal relaxation.

This use of a semicolon is awkward, because it would not normally be used in this fashion. On the other hand, it makes the meaning very clear. Sometimes, otherwise awkward punctuation is necessary to make meaning clear—and conveying meaning is, ultimately, more important than how it's conveyed. But only if there is no other way of doing so.

Note that a comma could also be used, but using a comma for only two list items is even more unusual in this context than a semicolon.

If the list contained three or more items, then (depending on the nature of the items) a combination of a colon, commas, and semicolons would be the normal way of punctuating it to avoid ambiguity.

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Note that the sentence as written can also be interpreted a third way that has not yet been mentioned:

3. I want to discuss the inhibition of reflexes and skeletal relaxation.

In this interpretation, there is only a single thing being discussed.