of a 51% attack is to generate the longest blockchain, yes. Please see here under "attacker has a lot of computing power"
A 51% attacker has to maintain enough computing power to beat the network to continue the attack. It would be pretty obvious quickly if such an attack started. Although I don't mine, even I'd jump in with other "bitcoin defenders" for example to increase "honest network" computing power. At some point I think it will be infeasible for any single entity to amass enough resources to beat the world population using/defending Bitcoin.
Transactions would be disrupted during a 51% attack, but the "official blockchain" is really only what all users say it is. By default it's the longest chain. Upon an attack people might agree to go back to the block just before the attack, or if need be, back to a checkpoint.
You're right about a difference between accidental and malicious transaction nullification. To address "accidental" ones it's common knowledge not to consider a network transaction valid until it has 6 confirmations. It's exceedingly unlikely a transaction can be nullified after 6 confirmations, however, you can wait even more if desired. The higher the number of confirmations the more unlikely it can be nullified.
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