In the thread Arima links to (from 2008) I say it's pronounced "see-rah"... but since then I've started saying "skirra" myself, because almost everyone I've met who looks at "scirra" written down said "skirra". So I caved and started saying it that way myself.
The thread's still right about where the name comes from: merge sci and cirrus to get scirrus, but scirrus.com was taken, hence scirra.