Your legal interpretation of that case is incorrect, and reflects the situation pre-Merrell. This case changed that situation.
That case changed nothing. From JO 7110.65S Air Traffic Control, Change 2, dated 3/12/2009 and valid through 8/27/09:
2-4-3. PILOT ACKNOWLEDGMENT/READ BACK
a. When issuing clearances or instructions ensure
acknowledgment by the pilot.
NOTE-
Pilots may acknowledge clearances, instructions, or other
information by using “Wilco,” “Roger,” “Affirmative,” or
other words or remarks.
REFERENCE-
AIM, Para 4-2-3, Contact Procedures.
b. If altitude, heading, or other items are read back
by the pilot, ensure the read back is correct. If
incorrect or incomplete, make corrections as
appropriate.
Merrell in fact read back the clearance, and was not corrected.
Merrell in fact read back a clearance issued to another aircraft. The controller in fact did not ensure acknowledgment by Merrell of that clearance because he did not issue it to Merrell. The controller did not correct Merrell's readback because he did not receive it, it was blocked by the readback from the aircraft to which it was directed.
Initially, in accordance with many years of precedent, the NTSB sided with Merrell and dismissed the case. The FAA appealed to the US Court of Appeals, and the Court of Appeals said the rule means what the FAA says it does. The case was returned to the NTSB for reconsideration, and the NTSB grudgingly abided by the court's decision and sustained the violation.
Read
all three NTSB Orders on the subject and the actual court case to understand all this.
http://www.ntsb.gov/alj/alj/O_n_O/docs/aviation/4530.PDF
http://www.ntsb.gov/alj/alj/O_n_O/docs/aviation/4670.PDF
http://www.ll.georgetown.edu/FEDERAL/judicial/dc/opinions/98opinions/98-1365a.pdf
http://www.ntsb.gov/alj/alj/O_n_O/docs/aviation/4814.PDF
I've read them before, I understand them, it is you that does not.
If Merrell v. Administrator has changed things in the manner you believe, there should be cases where pilots have been violated after an incorrect readback that was acknowledged by the controller but not corrected. Do you know of any such cases?