I was thinking of writing in an email that
Joe was kind enough to do XYZ for me
but when I read it, it stroke bad to me in terms that it sounded like implying that "usually Joe is not enough kind but exceptionally this time he was and he did what I asked for". What I actually want to say is quite the opposite and that Joe was just helpful. Am I right to be afraid of being misunderstood by using this phrase?
Yes, it can be misunderstood. But that's not because of the phrasing; it's because sarcastic intent can be conveyed using the same words as the 'plain' intent.
For example, if someone split some milk, a sarcastic remark might be "Oh, well done." They might do an 'eye roll' while saying that. On the other hand, if the person carrying the milk successfully brought it to the table without spilling a drop, someone might genuinely remark, "Oh, well done." They might clap their hands at the same time. Note that both remarks are identical, and you need other elements of the context to disambiguate the intent.
In your case, "kind enough" conveys the positive notion of Joe doing something out of his kindness. It doesn't ordinarily reflect badly on Joe, unless the context warrants it. For example, if Joe kept delaying a simple task and now finally does it, someone might use your quote in a sarcastic manner to call attention to how long it took.
