Fpga miners will naturally continue mining i guess.
As a gpu miner who does Not pay for elect i am mining just as long as it is worth my time. For example i just RMAd a card
Which cost me 15 dollars for a processing fee as well as shipping, crappy sapphire 5830 company, and if this happens more as time goes on with shrinking profits i will say it is time to quit. Now add in costs for elect, if i was paying it, and i could see many people quitting.
The "marginal miner" being forced out is a different discussion than the "broken" transaciton fee issue. In time FPGA will displace GPUs. It will take time but it will happen. GPU are 2MH/W to 3 MH/W. Underclocked and undervolted running optimal rig you are still <5MH/W. 45nm FPGA are 20MH/W. By 2013 28nm FPGA products will be out getting 40MH/W (thats a GH/s on 25W). If someday someone made an sASIC @ 28nm you could expect >100MH/W. With custom ASIC 200MH/W+ isn't unrealistic. 40GH/s per chip @ $80 and 20W is possible @ 28nm. From there it will only improve with Moore's law. GPU mining will end just like CPU mining has all but ended. I "think" we are still many years away.
The transaction issue is different one. Imagine there is no subsidy all you get paid on is transaction fees. Would you exclude a paying transction? You are already solving the block. The amount of extra work to include another transaction is negigble. In other words including 100K transactions is only marginally more difficulty than including one. If you are doing the heavy work of solving a block (who's difficulty is unrelated to # of transactions) you might as well include all paying transactions. Excluding a free transaction is a simple choice and in time most economical miners will do that. Excluding a paying transaction never makes sense. If you exclude it when you solve the block you get paid less. Someone else incldues it and when they solve a block they get paid more. No matter how "cheap" the transaction fee is 0.01 BTC, 0.000001 BTC excluding it simply means doing the same amount of work for less revenue.
Current transaction fee rules allow a fee as low as 1 satoshi (if no anti-spam rule applies). Given that a user can expect most/all of hashing power to include their transaction in a block for 1 satoshi so why would they pay more? A miner can expect other miners to include a paying transaction if they don't so why would they exclude it? In time you can expect (non-spam prevention) transaction fees to settle at 1 satoshi each. Which puts revenue at a negligble amount and will make almost all mining uneconomical.
This can partially be solved IMHO by having a minimum fee. Free transactions are still possible but if you include a fee it must be at least x.