In your first sentence, the use of the progressive aspect is not at all strange , on the contrary, it gives greater impact to the warning, as if the picture of the process of you doing something stupid were "forced" before your eyes here and now. "You will do something wrong" is more neutral and flat.
Newspapers use such constructions as well:
- Chelsea have been told they will be making a mistake if they let Willian leave the club on a free transfer. (Mirror.co.uk)
- It also warns that the UK will be making a mistake if it seeks to set itself up as a rival to the European Union on foreign policy... (the Guardian).
- Whatever we choose to do, we will be doing something wrong (the Guardian).
Your second sentence,
You would be doing me a great kindness if you agreed to help.
is an example given by M-W (and other dictionaries) in its definition of "kindness".
The emphasis is on the immediacy of the need: You would be doing me a great kindness now, on the spot. The use of the progressive is again meant to have greater effect on the listener, and that's why people prefer to use it rather than the "would do" version. "You would do me a great kindness " is not incorrect, just less strong.