Hmm. I guess the first question is who replaces Joe Johnston as head of the ANV once he gets wounded? There aren't that many names who stand out at this point of the war, and most who did were still embroiled in the Corinth campaign following Shiloh.
The Peninsula Campaign would have evolved differently without Lee, because the reason the Confederate Army converged on Yorktown was because of Lee.
In the April high command conferance to decide what strategy to employ to counter the threat of McClellan on the James Peninsula, Joe Johnston had argued that all troops on the Peninsula and at Norfolk should be ordered back to Richmond where they would link up with his army and reinforcements from the Carolina's and Georgia at which point they would be able to meet their enemy on equal or near equal terms, perhaps being able to engineer local superiority, and defeat them in detail.
Lee, on the other hand, argued that the longer the Confederates kept the Federals away from Richmond the more time would be available to train new recruits, manufacture or procure weapons and ammunition, and to concentrate forces around the capital, and therefore the better strategy was to conduct a stage-by-stage withdrawal from Yorktown designed to delay the Federal advance to buy that time then counter-attack from a strengthend position near Richmond.
Without Lee there's no guarentee Seven Pines/Fair Oak's would even happen let alone that Johnston would be wounded and circumstances the same for some other replacement - admittedly the chances of Joe Johnston getting badly wounded and forcefully removed from command are still pretty good (because he was a notorious bullet magnet who Winfield Scott once memorably described as having a knack for "getting himself shot in every major engagement") but that doesn't necessarilly mean it'll happen.