It seems that there is a rule (GM6) that allows your driver to use her wheelchair in the Alliance Station. If you have her in her wheelchair and use another member to push her to the station, you should have no problem. It seems that FIRST has to be more liberal with their allowance of mobility aids in the alliance stations because of this rule.
Dave
P.S. FIRST has spoken on the E-Stop issue. According to team update 9, if you press the E-Stop button during Autonomous mode, your robot will be disabled not only for the duration of the autonomous period, BUT THE FIRST 30 SECONDS OF THE HUMAN CONTROL PERIOD!!!