I don't think you actually lose any science if you transmit stuff back. Based on what I'm seeing, you've got a number that's the total amount of science a given part can give you for a given location.
Example(numbers might be off slightly, doing it from memory, but the theory is correct as I've watched it happen in several places):
Using the Materials Lab in orbit of the Mun can get you 100 science total. You can use the lab and then return it to Kerbin for all 100 science, or your can transmit for 20% of that, which would be 20 science. The other 80 isn't lost, it's still there since you can transmit again for another 20% of that 80 which gives you 16 science and leaves 64. Transmit again for 20% of that and you get 12.8 science, leaving you 51.2 science. You can keep doing this, shaving 20% off the remaining science each time, for as long as you have power available. Now, if you keep doing it it will inevitably leave you with a small remnant of science, since you can never collect it ALL if you just keep shaving 20% off of it, but if you transmit enough, you can end up with a number of remaining science left that's so small it'd be thrown away by the game anyway when rounding numbers.
It is tedious, requires a lot of clicking and requires some sort of power source to keep your batteries charged through all this inefficient transmitting but you never REALLY lose anything and it allows you to collect the science from multiple places with one vehicle. I just sent a probe to the Mun which got high mun orbit, low mun orbit and landed in a crater on the far side and researched that. With both the materials lab and the goo canister, it was very profitable science wise.
EDIT: I should have mentioned, I have strong suspicions that whatever science you DON"T transmit back in a given mission, can simply be grabbed in a later mission either through return samples or transmission. More tests will have to be done on this though.