The same rule would apply to other writing systems, or to secret codes: even if a character knows the language and is literate, that only means they are able to write that language in the script they know, not some other script. Which leads to the issue of semi-literacy, or partial competency in a language in general. How would I handle that?
As you can no doubt guess from my avoidance of skills, I don't want to approach language competency or literacy from a skill-system approach. That is, I don't want to handle languages this way:
Player: I tell the orc to step aside from the door and let me through.What I'd rather do is treat communication barriers as slow tasks or risky situations. I've posted before about how people without a common language can (and have, historically) communicated about basic needs; the main problem with using gestures or a tiny vocabulary of common words is that it slows things down. Assuming that two people speaking a common language take 1 round to exchange 1 round's worth of conversation, adjust the actual time needed using the "Degree of Change" and "Time" columns on the Tasks and Time Table as a guideline: being semi-conversant means the character takes 3 times as long, and having no common language at all means 5 times as long. Add +1 if either party has High Intelligence, subtract -1 if either has Low Intelligence.
GM: The two of you don't speak each other's languages very well. What's your Intelligence? (Rolls a d20 secretly.) You think he says, "I'll take a bribe."
Player: I pull out some gold coins.
GM: While you fiddle with you coin purse, the orc yells something you think means "betrayer!" and attacks you!
Similarly, semi-literate character take 3 times as long to read written instructions, as long as they're in a known language; it takes 5 times as long for a semi-literate character to read something in a language they only know a smattering of words in. Thieves using the Read Language ability to decipher maps should take 3 to 5 times as long as well; the same goes for the sage.
In certain situations, there's a risk to not being able to speak the same language. Any kind of negotiation, for example, might go awry; just use the Avoid Accident roll (4 or less on d6) to avoid miscommunication, adjusting for Intelligence of both parties: a failure means a -1 reaction. Some forms of bargaining with gestures may avoid this problem. In combat, hirelings who don't speak a common language will have delayed reactions to commands; roll the Avoid Accident roll for command control every 3 rounds or 5 rounds instead of every round. Any time there is a similar Avoid Accident or Avoid Danger roll to avoid something going seriously wrong, add +1 or +2 difficulty to the roll if there's a language barrier.