I've found two potential solutions to this:
Minimize the Nav Ball - this prevents shift from activating the thrusters
Double-click to focus - If you can see an object, you can double click to focus on it.
Note: With Version 1.2, the functionality of antennas was changed a lot and more antennas were added. This answer might not be very useful anymore.
With version 1.0, the antennas were rebalanced. But the stats listed on the construction screen seem to be misleading, because they have little relation to their actual performance.
As an experiment I tested transmitting the atmospheric analysis experiment with each antenna and measured the energy and time (without unfolding animation) it required.
Antenna | Mass | Cost |Energy | Time
------------+------+------+-------+-----
16 | .005 | 300 | 1200 | 60s
DTS-M1 | .03 | 600 | 1200 | 35s
88-88 | .025 | 1100 | 2000 | 10s
As you can see, the antennas later in the tech tree have a higher transmission speed. The fastest antenna - the 88-88 - requires more energy than the other two to transmit the same results.
Often the limiting factor when transmitting is energy supply, not transmission speed. To really make use of the 88-88, you need more battery capacity and/or a lot more energy sources which means more mass to carry.
That means when timing is not a concern, the first antenna, the Communotron 16 is usually the optimal choice because it has the least mass and is the cheapest.
The only case where it might make sense to choose a faster antenna could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver.
By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.
Best Answer
Since version 0.23, the Mystery Goo Containment Unit and the SC-9001 Science Jr. can not be reused after you transmit their science data, unless you have a Mobile Processing Lab on the vessel (or dock with one which has). The MPL can "clean out" these experiments so they can be used again (It can also "process" any science data so you receive more science through transmitting them). You find these option when you right-click the MPL. Note that both of them require a lot of electricity, so your space laboratory should be equipped generously with batteries and solar panels.
Update: In current versions (since 1.0?) astronauts of the Scientist class can also reset these experiments while on EVA. To do so move the Astronaut very close to the part, right-click on it and pick the appropriate option.