If I make an email operational, can I still exclude unsubscribes in the smart list? Or does making an email operational bypass that? We just want to make it operational to bypass the marketing suspended, but still exclude unsubs.
You absolutely can make whatever exclusions you want in the SL. No one will get an email who doesn't qualify in the first place.
As pointed out above, operational email behaviour and Smart List qualification are independent functions of Marketo.
A smart list will find everyone that matches the filters/criteria you specify.
An operational email send will send to everyone that the smart list finds.
If you don't look for people who have unsubscribed in your smart list - the operational email won't send to them.
One exception to your statement: An operational email will still not be sent to an email that has been marked invalid.