Are you sure you're losing half your EQM? I thought the booking classes for RTW fares were in buckets that were 1:1 or better.

As to your question, you can stop your RTW in the middle, as long as you make sure to leave a long enough stopover. If you're really nervous about it, you could book it on another carrier, but I don't believe there is anything in the RTW rules prohibiting it.