Without actually seeing the layout it's difficult to suggest the best way to approach this. Certainly trying to rerun the control lines so that they cleanly run under the dodger along with the other halyards and mainsheet sounds like a plan.
I don't remember the exact configuration of the E30+ cockpit, but another possibility might be to relocate the traveller/mainsheet assembly towards the end of the boom, behind the dodger. This does complicate the cockpit area a bit, but avoids the issues you have now, and as an added bonus makes trimming the main much easier from the cockpit (accessibility and mechanical advantage) This would be a bit of a project - you need to do it right with the proper fittings and attachments.
A friend has an E32-2, with a cabintop traveller and the control lines do run through the dodger windows. The traveller is quite short and I suspect he doesn't make much use of it.