I had to install spyder during beta... no problems... I also installed jupyter console and jupyter notebook and a bunch of other things. No 'pinned' issues.
When Pro 2.2 (non-Beta) rolled out, I got to practice doing it all over again... this time it took me all of 5 non-waiting minutes to get it done.
I have been working all along as people wait until a 'fix' is made to the cloning. Unless you are way out there in terms of python modules, anything in the Anaconda suite is pretty safe. If things go 'south', conda is pretty smooth about removing stuff.
So in short... until they install spyder, jupyter console and jupyter notebook by default... you can either wait until someone else fixes stuff, or install your IDE now.
The worse case scenario?? What is your? I have none