The last few games I've played I've turned off weather so I don't have to deal with dormant plants. A couple other things you could do, like Candy mentioned - bring them inside as in transfer them into pots.
Build a "green house" for the plants and trees. You may need to use MoveObjects to place the plants inside the green house. Unless you've got the green turf like stuff from Into the Future, I believe. I've never used it. So I don't know if the turf like stuff works.
Also with using the green house after the plants die you may need to replant some where outside the green house and then use MoveObjects again to place them inside the green house.
That has worked well for me when I have had weather turned on in my games.