To start, EFF doesn't support patents.
The http://defendinnovation.org site is EFF's attempt to evangelize the idea that current patent system is broken and gather support for changes that would improve the system a lot.
Any lunatic apparently can start a petition on change.org and some did because EFF's (realistic) position isn't radical enough for his taste: he wants abolition of software patents.
Now, personally I would prefer abolition to the reform ideas proposed by EFF but this is not about what is better. EFF probably has to consider things like: does a given idea has a chance of being implemented by congress.
EFF is fighting the good fight. They try to improve the awful patent system and I have no doubt they do it in the best way they can.
Nothing stops the guy who created this petition to evangelize abolition of software patents. He can even start his own foundation for defending internet and civil liberties.
But attacking EFF in this way is harmful. He brings nothing positive to the table and can only derail EFF's efforts by instigating infighting among people who want the same thing: fix broken patent system.
Finally, one can support EFF's reform as well as patent abolition. We would be better off with either one.
Just don't attack EFF for trying to do something about patents.