The traditional scenario is the 51% attacker is using his hashing power to somehow directly profit. The disincentive in that scenario is that 51% hashing power will net more in mining than in double spends.
Yes and that is a powerful disincentive. Also getting away with widespread fraud will leave trails in meatspace and that likely will get the attacker caught. I believe the risk of an economic 51% attack is highly improbable. As economic activity increases, the value of BTC will increase and the value of the hashing power required to have 51% will also increase. The network is essentially self-protecting.
The scenario you describe is the 51% attacker is spending money to destroy bitcoin without a direct profit incentive (there incentive may be indirect like a competing monetary regime). With 51% or more of the hashing power the attacker will secretly mine for 1 day to two weeks then drop a new chain on the internet.
Exactly. The amount of time can vary but with 51% of hashing power it is a mathematical certainty that eventually the attacker will have a longer chain. One thing to note is that the attacker can't go back in time. Meaning if an attacker started now they could only affect future blocks. Going back in time requires exponentially increasing hashing power because the attacker is essentially starting behind.
This new chain will contain zero transactions, or non other than what directly benefits the attacker.
The attacker could generate blank blocks but it would create more destruction to create double spends even if the attacker doesn't benefit. An attacker for example could place 10,000 orders at various Bitcoin merchants using names & addresses harvested via "win a free gold coin, free PS3, free ipad, etc" websites. These patsies would simply exist to be destinations for merchants goods. The attacker could then double spend the network reversing all those transactions and the merchants would be out hundreds of thousands of coins. The resulting chaos would likely create a lot of negative press when merchants contact these "contest winners" asking for merchandise back. Also remember when the transaction is reverse it also reverses any follow-on transactions. Attack sends 100 BTC to you. You pay me 20 BTC. If attacker reverses his transaction it also reverses mine (as you never had the coins to pay me). That creates further chaos as there is no a conflict between you and me.
So even if the attacker has no economic gain using double spends would cause massive chaos and economic losses for participants.
The honest nodes will have a fresh pool of transactions to confirm and 49% or less chance to get the next block. Do honest blocks eventually get rejected because the attacker is able to perpetually rewrite the chain with empty blocks?
It is unlikely it would require attacker continuing in perpetuity. The reversal would wipe out all miner profits for those reversed blocks. Imagine if every miner received 0 BTC income this month but still had hundred or even thousand dollar power bills. Miners would quit in droves. Merchants would stop accepting Bitcoin as fear of the reversability of transactions spread. Bitcoin prices would crash and the attacker could profit by shorting or using put options to gain when Bitcoin prices decline.
However yes any good blocks will eventually be overwritten because the longest chain always wins. So while in the first block the defenders (if they have 49% of hashing power) will have a 49% chance of being ahead the attacker will make the alternate chain in private. If the defenders get lucky and get 2 or 3 blocks ahead he can simply restart at the current block attempting to win the next race.
Eventually the defenders luck will break and their chain will fall behind. Once the attacker has a longer chain (with a solid lead that is improbable to overcome) and enough transactions ready to double spend he can broadcast the alternate chain, clients will replace the good blocks with bad and in doing so reverse all those transactions and render all other transactions unconfirmed.