Either I don't understand the problem or you are overcomplicating it. As I understand it, you have this tube/flap in a closed environment. If the servo motor is also in that environment and sterilized before being placed in the container, where would any contamination come from?
As for the seal, as long as its made with a material that has some compliance, a servo motor should be able push it tightly enough against the end of the pipe so that even with power off, you'll maintain a seal. There's enough gearing in a typical servo that it is very difficult to turn the shaft by hand.
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If you want a completely manual solution, two cheap syringes connected by a tube of water make a pretty good hydraulic actuator. One syringe on the outside, one on the inside connected to the door and the tube passes through a sealed opening on top. It may need to be spring loaded to work well though.