You are correct about NaOH degrading the RNA. What you do when you crosslink to
a POSITIVELY charged nylon membrane is the following: soak in 0.05 M NaOH for
5 minutes followed with a couple of washes of 2x SSC.
The conditions are not harsh and limited in time.
In fact this treatment was shown to result in more sensitive detection of message when
compared to UV crosslinking.
An article on this appeared in Biotechniques either this month or last.