I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Issue:
Not able to install service fabric runtime version 9.1.1653, getting null reference exception
Solution:
KtLogger and LeasLayr was running which was not allowing deletion of C:\Program Files\Microsoft Service Fabric folder.
After running below 2 commands and deleting C:\Program Files\Microsoft Service Fabric folder it resolved the issue.
Open an elevated (as admin) command prompt
- run this command
sc.exe stop KtlLogger
- run this command
sc.exe stop LeasLayr