Well first of all, for Paxos to survive 2 failures it would need 5 nodes; Paxos won't work very well for smaller networks, and a bad network design [or lack of good maintenance] could take out a majority or all of your nodes, making the whole system worthless.

Second, most systems don't need atomic write operations to succeed across network partitions, when network partition is even a concern (for general operations), which it isn't usually. If your network is partitioned, you can't really "decide" anything until it un-partitions, at which point you don't need to come to consensus if you have simpler methods of solving discrepancy - like using a higher level decision process than block-level or database-level. Even after the discrepancy is solved, network-wide changes may have invalidated the initial partitioned operations. Paxos tries to over-simplify a complex operation.

When it is a concern, application design often trumps system design in terms of reliable operation. It completely depends on your network, system, platform and application design. In general, you won't need Paxos to reap the benefits of distributed systems, and synchronous systems will give you more benefits and less headaches.