How do you sump fuel when it's raining outside?
AOPA has a good article about checking fuel:


  ... check the fuel caps and replace worn, brittle, or cracked seals
  that can allow rain to seep into the tanks.


You cannot be 100% that the fuel does not contain any contamination. If you risk that by putting the sample fuel back in the airplane (debatable topic) will add more water in the tanks, then simply don't do it.

I guess since many flight schools offer wet rentals, they don't want to waste a drop of fuel. But it is okay to do that, so that their aircraft and your life are safer.

Update

There are many arguments about putting sump fuel back in the tank. Many people say that a GATS Jar is there to capture the contamination and then you can put it back in the fuel tank. In Cessna training material, they use a container where you can put sump fuel. At many places, there is a fine for throwing it on the ground.

So in case of rain, the best option is to put in such a container. However, if it is raining that hard with strong gusty winds, I am sure taking care of sump fuel should not be your problem.