I do not think this has as much to do with can vs. could. A rhetorical question doesn't have much to do with grammar and more so the context and tone of the question.
A rhetorical question is asked to create a dramatic effect, not get an actual answer. And with rhetorical questions or sarcasm, there will always be room for misinterpretation that normally has nothing to do with the words in a sentence and more to do with the context and tone.
Now for the actual difference besides the rhetorical question part. "Can" refers to your current ability in the present, and "Could" is used in the past tense.
Assuming the context in which these are spoken have the proper tone to convey a rhetorical question, these sentences do have different meanings based on grammar.
He has questionable behaviors. How can I defend him?
This is happening in the present. You are being asked to defend this person in the present, and this is your response.
He has questionable behaviors. How could I defend him?
This already happened in the past. At some point in time, you were asked to defend this person and you did not.
If you want your rhetorical question to be as close to your context of "I cannot defend him.", this is present. Go with "He has questionable behaviors. How can I defend him?" and make sure there is proper tone when asking so it comes off as rhetorical.