Hi Jay!
I'm glad you're considering Thonny for your classes!
About breakpoints -- I wanted to do away without them in order to keep the debugging model simpler, but they may appear in a future release. But did you try "Run to cursor" from "Run" menu? Maybe this can be used instead of breakpoints?
About variables -- I found the problem you described to be great opportunity for explaning why it's useful to avoid star-imports. But your message made me consider showing imported names in the end of the table or with different color or something like this.
In general, my main focus has been to visualize Python's "notional machine" as clearly as possible. Seems that in some cases this is in conflict with efficient use of the IDE. I don't worry myself too much about it because I expect my students to move on to a more powerful IDE once they understand the principles of procedural programming.
best regards,
Aivar