IMHO the run troubles in San Fran were a combination of fatigue and having a rookie MLB.
Having ET as the single high safety gives us 10 men up front for strong press coverage and essentially 8 men in the box against the run. ET has the speed to cover the whole field back there if a play breaks open. I don't recall any tackling issues with him. Hell, he took Gore down one on one a couple of times Thursday night. Unless we're playing nickle, dime, or Bandit, ET doesn't need any help back there.
Overall, though they may seem to mis-use ET on occasion, I think our D schemes have been pretty effective.
IIRC, ET was up close to the line on some plays.