Patrick: Your assumption is wrong to start with. The bug is not in GTK+, but in Eclipse.
Starting from 2.18 on, GTK+ changed some of its internal behaviour (google for "client side windows"). This change is intentional, and needed for other development. It doesn't make any difference to programs using GTK+ correctly, but it makes problems with programs that use GTK+ in weird ways, making wrong assumptions that only accidentally worked in the past. So, to ease the transition until those programs get fixed, an environment variable has been introduced to simulate the old behaviour.
So it's really up to the eclipse guys to fix their code, and to make sure they set this variable as a workaround until then in their own distribution. Ubuntu doesn't have any influence on that.
The only possible workaround that could be done in Ubuntu was to set that variable globally by default. That may break (correctly working) apps, just in order to work around broken ups from 3rd party sources. Doesn't seem like a good idea to me.