I have the Digigami MegaPEG encoder. It can produce some really nice results if you are willing to wait for it. Unfortunately, the encoder is not very fast (even on a quad g5), but if you have the time and want mastering quality, then it is a good product. Plus, it has access to just about every option available in the MPEG spec, although this can be a great or terrible thing depending on if you know what you’re doing.
As far as your current encoding issue… are you sure it is Compressor that is causing an issue with the interlacing? It may be because you are playing your content back on an progressive monitor. Interlacing on 480i is much more noticable than on 1080i (which I assume is the res of your HDCAM source). I would suggest you try deinterlacing your 1080i content to 480p when encoding, if you haven’t already. Also, if you use Windows XP, then another encoder I would recommend for MPEG-2 encoding is Canopus ProCoder. If the mac is the only option, there is also the MainConcept encoder. It doesn’t have the “mastering” level quality of Digigami, but it is much faster and for the majority of my projects I find it more than suitable.