I managed to avoid a similar situation, also with a CO/LH itinerary, by using the following tactic:

1. Booked the itinerary with CO, with my OnePass number.
2. Created a brand new United Mileageplus account (never had one before).
3. Flew the outbound with CO, CO metal.
4. On the return trip, which had a stopover in London then LH via Frankfurt to Tel Aviv, after I had checked in, and used the *G lounge with my CO *G boarding pass, I went to a service desk and asked for my United number to be put on the reservation instead of my CO. They reprinted me a Boarding Pass with the United number.

Here's the magic: United has a better deal than CO for LH flights. On United you get 100% EQMs for all or nearly all of the fare classes.

So... I ended up with most of the miles and EQMs in my CO account, and with about 2000 odd miles and EQMs from the LH flights in my new United Mileageplus account. Happily, when we hit 2012, those accounts will be merged. So by doing this crazy work-around I end up with 100% EQMs not 50%.

It's an absurd situation, and I totally sympathize with the OP's frustration, but during calendar year 2011, that is the way to play the system!