Bitcoin deposited with MtGox or in transit are safe. We disabled deposits because this condition makes it easier for an attacker to perform some kind of attacks Bitcoin is designed to prevent. Once the situation is back to normal, we will resume accepting deposits, and all deposits done in the meantime will be confirmed too.
UPDATE: Miners are encouraged to downgrade to Bitcoin 0.7.2 - at least temporarily - to push the correct blockchain forward. Once the correct blockchain is longer than the 0.8-only blockchain, we will be able to resume bitcoin transactions.