As I understand, Ian's writing a virtual machine (VM) for ATs. That means a place set aside for ATs to perform their calculations, and that means ATs won't be allowed to interfere with the rest of your computer. I think ATs will also only be allowed to send transactions from the account that they're "assigned" to, so that's another good restriction.
Pretty close - certainly an AT won't be able to "damage" the forger's computer (even if it has an "infinite loop" coded it is of zero concern) but at this stage I hadn't planned restrictions on which account an AT could send money to (although it is perhaps unlikely that we would be letting it say iterate all accounts).
In general the practice of spamming should be taken care of by the fact that all txs require a fee (and we could even increase those fees for txs that originate from an AT). Also understand that the Nxt AT won't be talking to the Nxt API but to a Nxt AT API to keep it safely "sand-boxed".