Can I average the two RMM values?

CAN you? Sure, nobody on here is stopping you.

Is it meaningful? Not really.

The RMM indices are two separate metrics corresponding to the phase (interpretable using a phase space diagram)

(Example from CPC)

If you want a more meaningful way to interpret the MJO, you can try $$sqrt{RMM_1^2+RMM_2^2}$$ which should be the strength of the MJO, or the angle between $RMM_1$ and $RMM_2$ (probably using something like atan2 in your preferred programming language.