You are absolutely right--that will happen.
You can do either of two things:
1) Get some plugs. They look like tapered rubber corks with a wing-nut attached. You put them in the return, the low drain (if you have one) and the skimmer to plug the lines. Then you open the pump strainer. For threaded outlets, you can also use a threaded plug. Remember to remove the eyeball or screen first.
2) You plumb in ball-valves to isolate the pump from those lines to clean the pump's basket.
1) is cheap but you have to do it everytime
2) is a little work but it make shutting down instantaneous.

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