There is not other block-chain with bigger combined work amount, so checkpoints in Bitcoin-qt are correct ones
How do you know that there is no other block-chain with bigger work amount?
Perhaps fork started right from genesis block, and was mined all the time at private cluster at super high-speeds (now on cluster of asics).
How we would select right chain? Well, Bitcoin is decentralized. And no small group of people should decide which branch is correct and which is not.
Checkpoints hardcoded in code were selected by small group of people.
But if Bitcoin is still claimed to be decentralized, not controlled by government, small group of people (which can be blackmailed, or forced by thermo-rectal cryptanalysis) - then only majority of users should have right to make decision.
Users should vote on which branch is correct and which is not. Bitcoin already has such voting mechanism - vote by computing power.
Of course hidden fork crunched in shadow is unlikely, and maybe checkpoints do not harm due low probability of such fork.
But they harm in other way - they compromise Bitcoin decentralization, which is in my opinion is the biggest attractive feature of Bitcoin.
Today they add checkpoints, tomorrow they could freeze BTC on your address, by adding small tweaks to validation routine (just like checkpoints validation).