Did you disable the global guess_indent option?
I don't know if what you're looking for can be achieved via the config file, probably others will help you here if my advise doesn't work. Let me share with you what my first thoughts were when reading your mail:
Open source software is usually developed by volunteers in their free time. As you can probably see, joe's development is stalled right now. I'm quite sad about it too. Noone knows if it will be ever continued (and when and by whom) or uses will simply migrate away until noone cares anymore. But complaining that "you fix it or I'll use a different editor" won't help here.
Reading your words "has been an almost perfect option up till now" made me wonder, the most recent version of joe is 5 years old, so I'm not sure what you mean by "now". There's hardly any way it could've become broken recently.
You mention that you'd even start writing your own editor. Well, take a minute to think about how much time you'd put into that. Even getting used to a different, actively maintained editor is way less work. Let me offer you two other alternatives which might save you weeks/months of your life:
You say you were perfectly satisfied with earlier versions of joe. They are still available, you can download, compile, and use them happily.
Joe's source code is there for anyone to edit. Even if you've never looked at it, take just a few minutes to see if you could change it to match your needs. The option you have trouble with is "indentc". Find all occurrences of this string in the source. Figure out what's the variable in which the value is held. Maybe it's also "indentc". Find where a value is assigned to this variable. Change it to hardcodedly assign a space, and there you are, you fixed it for yourself, and saved yourself months from writing your own editor.