Two problems here.
#1. There is now no traditional judicial standing for exoneration.
#2. Without exoneration, it now becomes significantly harder to place him over an agency.
Additionally, this will be seen by many as both capitulation, and a signal of Trump stepping down.
The 2 points you outlined are true.
By taking a pardon, it assumes a crime was involved. Also, Flynn will not be able to take a government job.
The plan was for Flynn to be eventually exonerated by the courts in Trumps second term. This tells me that Trump will allow Biden to become president if his team is unable to convince the Supreme Court that Biden did not legally win the election.
I want Trump to go scorched earth and invoke the Insurrection Act, nullify the fraud election, declare temporary Marshall Law and finally arrest and execute ALL the traitors (Republican and Democrat) that were involved in the election heist.
I smell the stench of Deep State on your post.