JSON::XS is not thread-safe (crashes mod_perl in production) and seems to have a memory leak (I see oob on apache after some time...)

Would it be possible to take mod_perl out of the equation, and instead have a daemon to do the JSON translation? Your mod_perl code could call the daemon and get back the object. The daemon could spawn a new kid to do the actual translation, which should obviate any possible memory leakage problems. I wrote something like that in 2007-08, and it worked really well.