Looks like you have a couple of issues. The pipe you show has no trap, or at least as shown. Without it, you should be exposed to the same gases as when you remove it to drain the floor.
My suggestion, aside from fixing the trap situation, would be to fill the hole in the foundation from the inside with hydrolic concrete. This should at least stop the inflow of ground water. Depending on the foundation construction when weather improves, you may need and or want to do additional work from the outside.