Desmond's system failure may not have coincided with the crash, since only the log printout links the two events.
This is seemingly confirmed in Seasons 3 episode 1 "A Tale of Two Cities" when The Others are first scared by a quake, assuming that's the system failure, then come out to see the plane crash
A system failure explains the extensive damage to other stations. For example, there may have been a time before the losties arrived that there was no fail safe. The electromagnetic anomaly grew out of control, and began to wreak havoc on the other stations. The Pearl had part of its roof ripped out, The Arrow seems too dusty and dirty to recognize, and The Staff has lights hanging from wires. No matter how strong a magnetic attraction is, the source object can not be damaged directly, explaining why The Swan was still fully operational. DHARMA may have decided that the damage done was beyond repair, and abandoned all projects other than The Swan, where they installed the fail safe and regularly initiated supply drops, to keep another accident from happening.
Unlikely; other damage was mostly likely caused during the Purge.
This is the actual event monitored by the men at the listening station. As the discharge has only happened once but the system failure has occurred two times and the men at the listening station saw the "anomaly" twice.