MetSox, as I'm sure you're aware, you've planted your lavender in a place with poor drainage.
Unfortunately, simple siphons won't work for such a situation.
I don't think you need to worry about root rot as a result of one flooding. Root rot is usually the result of weeks of standing in water. Your lavender can probably tolerate sitting where it is for a few days, but I wouldn't suggest that you push it longer than a week, if you can avoid it. I have lavender that routinely sits in very wet clay soil all winter, and it's doing fine, but I have the soil mounded into a berm to increase drainage.
If you think the soil will take longer than 5 to 7 days to drain to a depth of 6 inches, you should probably dig up the sprouts and plant them in a soil designed to drain rapidly (think cactus & succulent soil mix for a temporary basis), preferably in a raised bed or in containers. Otherwise, just leave the plants where they are, at least until the soil is drier. Moving them while the soil is very wet can cause as much damage to the roots as just leaving them where they are for a few days.
If heavy rains are a regular event in your area, you certainly will want to move the lavender to a spot with better drainage before next season. Or, just create a berm, as I have done in my yard.