Ben
As long as ponds above your watershed consist of BG or LMB fisheries, you will always run a very high risk of invasive species being introduced. The only way around this is to completely divert that water from your pond through levies, etc. I have seen this happen many times - cool water species fisheries are especially vulnerable to upstream fisheries and invasive introduction.
You can still manage a YP/SMB pond however you'll need to employ very aggressive LMB/BG population management strategies and may have to supplementally stock SMB and potentially YP to keep their presence viable. It can be done, just wanted you to be aware of what you're up against.
Draining, seining, and nuking is an option - but be aware unless you divert water from upstream ponds you're one significant rain event away from invasive introduction.