It was a problem for me too, since I only play good aligned characters. Nowadays I simply roleplay the beginning of the Main Quest slightly differently.
I will drop the amulet off since that was a promise made to a dying man. But once I've dropped the aumlet off, then that's where i take the break. This does take some selective hearing, but what my character gets from Jauffre is something along the lines of:
"Thank you for delivering the Amulet. Feel free to take anything from my chest as a reward. Then you can leave."
After all, you're an unknown ex-con, why would he trust you with such an important job, aren't the Blades much more suited to find and retrieve Martin?
Ofcourse they aren't, and thus after a while (this can be as long or as short as you want) you get a message from Jauffre asking you to go to Kvatch, since they've finally tracked down Martin. (I ignore the bit where he tells you where Martin is and RP they've lost track of him for a while, he wasn't that important up till now after all). Maybe Jaufre remembered that the Emperor asked you to find his son and his Blades are simply not destined to help him. Maybe tales of your deeds have reached his ears and he thinks you might be better suited for the job, or maybe he had someone following you/observing you and now finds you trustworthy. Maybe a combination of all of that.
There might be mods doing something similar, but just RPing it is easier
As others have said there are other points I can RP a break, leaving me free to persue my own goals. This way I can do the MQ at my own pace without any guilt