Absent the presidential pardon power, this check is available: As far as I understand, Congress can just pass in both houses and have signed by the President an act pardoning any specific individuals or groups of individuals. It's right there. Eliminating the presidential pardon would simply require the President to get two houses of Congress to agree to pardon someone in order for the President to sign it and make it effective. This would ensure that any pardons would be for clear problems that both Congress and the President agree with, and also make it so Congress has to take the first act.
It'd also stop those annoying pardons that are literally issued on the very last day of their presidency, because a President would need congress to pass it first before they sign it.
I think there's a very solid case for preventing the "lame duck pardons" as you mentioned...
Mainly, because once that layer of accountability of "I need to get re-elected, or at the very least, avoid impeachment" is removed, that's when those "time to let my buddies off the hook" pardons start flying fast & furious.
I've considered the congressional aspect you mentioned, but I don't think it solves the problem (at least in terms of a replacement), and I'll tell you why...
1) It's still going to be employed in a partisan fashion. No Democratic partisan congress is going to make a motion to pardon a well known Republican figure, and no Republican controlled congress is ever going to make a motion to pardon a well known Democratic figure.
2) If it's a collaborative solution (where a president has to do it with the approval of congress), it's going to be viewed as obstructionist when the congress is not on the same team as the Pres, and viewed as a farcical formality ("rubber stamp") when congress is on the same side as the Pres.
So all of the same challenges and perceptions of partisan bias will still be in full swing (just with extra steps)
Now, I have heard an option that I've heard described that I've liked (though I don't know how practical it is) that still has a multi-branch collaboration element.
There's a pardon board (similar to a parole board) comprised of 7 members.
3 appointed by the Senate Majority leader
3 appointed by the Senate Minority leader
1 appointed by the Senate Parliamentarian
(and each of those positions has to be confirmed through the same process as cabinet appointments)
The president has the power to send pardon referrals to that panel, but it needs a 4-3 vote in favor to "pass".
Ultimately, this is a sticky wicket because of the fact that the founders (despite having many awesome ideas about checks and balances), didn't have a great solution or remediation element to the fact that the judicial branch has an outsized amount of power compared to the other 2.
And the judicial branch is the only one for which there's no rigid tangible standard by which to "un-do" what they do. (outside the branch itself)
Plus, the branch is unique in that the "Supremacy Clause" doesn't fully apply.
A state level judge technically has the power to say "I deem this federal law to be unconstitutional, so this state won't be enforcing it for the time being"
No such dynamic exists in the other two branches.