I'm not clear on that first sentence: it reads as though L+ Free Speech should override Flag Burning ("should be illegal" = act as though Flag was at least M, if not C or C+ ??) and do something to the Terrorism charge. Based on your second sentence, though, I'd guess you want L+ Free Speech to trump Flag Burning (act as though Flag was L/L+) and make Terrorism similarly not-charged.
My understanding is that LCS!Terrorism = messing with the nuclear plant's red button. Not sure if there are other ways to get it in-game. Burning a flag generally only puts the burner at risk of physical harm (set self on fire), whereas messing with the reactor/nuclear waste could contaminate the whole city. (Not to mention possible consequences from the generator suddenly going offline. Example: Power outage throughout the southern US in summer = no A/C and heatstroke fatalities.)
I'd say endangering thousands/millions of lives really couldn't be justified under "expressive conduct", no matter how Liberal the justices are. Changing flag-burning is an decent idea, but LCS!jurisprudence might have somehow carved out an exception for flag-burning.