I have some programs that really don’t fair well with defense+ and instead of going through the options and reboot each time could there be an option to deactivate it or not even install it during setup?
you mean disable Defense+ ???
you can disable on CIS tray icon right-click option if that’s what you mean. ???
& if you want to permanently disable Defense+, you can tick deactivate defense+ permanently on:
CIS/defense+/advanced/defense+ settings/general settings
and yes, if you choose to install CIS-firewall only (leave the AV out), there will be another question asking whether you want basic firewall or firewall & defense+. if you choose the basic firewall, the deactivate defense+ permanently will be ticked by default. 
Disabling Defense+ doesn’t make any effect on the programs affected they just simply don’t run, there’s no warning or anything to let you know why either. Checking deactivate and restarting allows the programs to run again. One program that’s affected is remote administrator 3, free trial available for test if you want. With a few remote computers that I control via remote administrator defense+ activated during install is the difference between me using comodo vs another anti-virus.