OK. Now that I got that off my chest the answer to the OP is that you can never expect that McClellan would destroy Lee because that was never his intention. McClellan was scared to death of Lee and always expected that Lee was hiding this huge force just ready to pounce and destroy him.
This doesn't really make sense of McClellan's actions at Antietam, though. I'd agree that McClellan doesn't have a hard lock on exactly how many men Lee has, but as of late on the 16th McClellan has committed 1st, 12th and 9th Corps to attack and will send 2nd Corps over during the night. This means he's committed all but two divisions on the field to attack (Sykes and Richardson; he releases Richardson back to 2nd Corps when Morell arrives).
McClellan's concept of operations is to hit Lee from the north with a heavy attack and send a less powerful but still corps strength at him from the south, in an attempt to hit Lee and also cut off his retreat. The fact that it collapsed in a haze of "friction" (in the Clausewitzian sense) doesn't mean the concept of operation didn't exist in the first place, and what it means is that McClellan is keeping back two divisions that aren't committed to the attack.
This is an attempt to destroy that portion of Lee's army which is north of the Potomac.
As of the early afternoon, it is self-evident that the attack from the north has not been successful, but Franklin's five fresh brigades are able to keep on pressure simply by existing - they are preventing Lee's remaining force from turning on Burnside. At this point the thing McClellan could do to minimize his exposure if he fears Lee has a strong remaining force is to cancel Burnside's attack - this would create a situation where Lee can't direct his whole remaining force either north or south, since there is a threat from both directions.
Instead what McClellan does is to check on Burnside to try and speed him up, and order two of his last three uncommitted brigades north to join Franklin for an attack; Sykes' division is to be ready to advance on Burnside's flank.
This is an attempt to deliver a strong blow.
Only once Burnside collapses does McClellan stop making preparations to try and hit Lee further on the 17th, and this is because at this point almost McClellan's entire army is spent. He has a total of six fresh brigades in the north (Franklin's five plus one flank guard from 1st Corps), four and a half in the centre (Morell's three plus one from Sykes, along with Warren's tiny two-regiment brigade) and none in the south where Burnside has given way; the remaining thirty-three brigades on the field are either tired out from fighting or (in the overwhelming majority of cases) have been repulsed or routed.
McClellan does not know how strong Lee is; what he does know is that Lee has fended off attacks by approximately 60,000 men and seems to keep bringing up new reserves. Consequently McClellan opts to wait to attack when conditions are more favourable.
This is of a piece with his movements to South Mountain (which involve a fast movement from Frederick to hit at places where Lee is vulnerable, disregarding the possibility of another Confederate force south of the Potomac that might try and strike at Washington).
On the 18th McClellan seriously considers attack, but a number of factors (like the still-shattered state of 1st and 2nd Corps, Burnside insisting that he needs to be reinforced urgently, a serious lack of artillery ammunition, and the exhausted state of Humphreys' division when it arrives from Washington) mean that the attack is postponed to the 19th. On the 19th McClellan of course attacks early in the morning but the Confederates evacuated overnight.
Antietam does not look like McClellan never intended to destroy Lee's army. It looks like McClellan attacked hard when it looked like there was a reasonable chance of killing or mauling Lee's army based on the information he could know, and that when he stopped attacking it was because he'd essentially run out of reserves - perhaps he could have made one more two-brigade attack without risking the destruction of his army, but Lee has
three brigades that he hasn't even fired a shot with.
This isn't to say that Antietam was a battle that couldn't have come out a success - it's just that what needs to happen is a bit more coordination in getting over the Lower Bridge. A good way for this to happen would be for Reno to survive, since it seems that the loss of Reno harmed the articulation of 9th Corps and led to much of the delay. Have that and you have 9th Corps getting over the bridge hours earlier, which offers at least the possibility of the 9th Corps attack going through well before AP Hill arrives - combine that with the two brigades of Morell (historically sent) and the five brigades of Franklin making an attack at the same time and that
could overpressure the Confederate lines.
Of course, it's not like cases where 43.5 brigades broke 39 brigades exactly abound in the Civil War...