I would charge the late fee. It's the beginning of the relationship and its up to you to set the tone. I would look at it as business - you can't call your credit card and expect them to not charge a late fee because you just didn't have the money! Plus, at this point, if it does end, you don't have anything invested.
If you decide to waive the late fee, then I would explain that it was a one time courtesy waive.

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