As you stated, you can use a separate program to trace your drawings, then import into MoI and extrude. I have used the trace function in Corel Draw with success, however you need a fairly clean drawing to start. By clean, I mean that in order to extrude you need closed shapes (no gaps).

The best program to use in my opinion is WinTopo (a free version is available). WinTopo was designed to convert old hand-drawn maps to vector format for electronic storage. The nice feature of WinTopo is that you can set parameters to "heal" small gaps in lines. It has a very intelligent trace algorithm and gives the best results of any trace program I have tried.

WinTopo also has a command line interface in addition to a normal Windows UI. This means you can launch WinTopo, load a file, set trace parameters, and export the result from within another program. This might give the possibility to interface to MoI with a script.

If you post a sample drawing I'll see if I can give a MoI result via WinTopo.

Ed