I think you're overestimating what applicants are expecting here. Obviously a form rejection opens up a lot of problems, but a form acknowledgement doesn't share those issues. Something as simple as "Thank you for your resume, we will review it and contact you if it appears that we may have a position suitable for you." Stress on the "will review" so that it's clear the applicant hasn't been considered yet, favorably or otherwise.
In particular, I consider this worthwhile for resumes submitted at various career fairs. The process employed there frequently comes down to handing over a paper resume and being told "Thank you for your resume, we'll digitize it and put it into our system." This is far from reassuring, particularly after the first few times you get clear proof that your resume was never digitized at all. A form note simply acknowledging the submission provides your applicants with confidence that their resume is truly in your possession and a better feeling than applying to a black hole.
In particular, I consider this worthwhile for resumes submitted at various career fairs. The process employed there frequently comes down to handing over a paper resume and being told "Thank you for your resume, we'll digitize it and put it into our system." This is far from reassuring, particularly after the first few times you get clear proof that your resume was never digitized at all. A form note simply acknowledging the submission provides your applicants with confidence that their resume is truly in your possession and a better feeling than applying to a black hole.