According to the compatibility list Ninja should be compatible with Abit AB9 Pro. Either Scythe tested it or someone of the users reported compatibility.
Ninja PLUS Rev. B Compatibility List
The capacitors can be a problem - it definitely depends on their height. Also the quite high chipset cooler between ATX IO shield and CPU socket could be a problem. Exact height would be necessary to make further suggestions.
I see big problems when installing the Ninja with Retention Kit but with Pushpins it should work if the mentioned components aren't too high.
Fanless with E6700 is possible if you ensure a very (!) good airflow in your case. Unervolting@2,66 Ghz is no problem with this CPU and a very cheap method to decrease temps. You should be able to use less than 1,16V for a stable E6700. My E6700 runs with 1,19V @ 3Ghz.
But as I can see with 4 120mm fans the system is far from "passive" so you could also connect a fan directly to Ninja.
I am running a rather "hot" system (E6700@3,2 & Geforce 8800 GTS (G80)) with a total of 2 fans @ 800 plus temp regulated power supply fan. If you do not plan to overclock as you mentioned it could be possible to run your system with 1 fan for the Ninja and the PSU fan. Depending on the case layout.
Bye Oli