I used a Beogram 6000 with my Beosystem 6500 for a long time before I found a matching BG6500, and I was very happy with it (still am, it is connected to tape 2 now... ).
There's a switch for turning the CD4 decoder off, but it isn't really needed since the decoder will play in regular stereo anyway when it cannot detect the CD4 carrier from the record. The extra two output lines don't matter either, you can plug it into any input socket that accepts line level signals.
The original MC6000 is likely to have seen its best days. The BG6000 itself is quite old as well though, and may need attention or service sooner than the modern alternatives.