Confederate strategy for the Peninsula Campaign had always been to fall back to the vacinity of Richmond so as to negate the effectiveness of the Federal Navy to outflank the Confederate Army via the York and James Rivers.
Further, the time bought in delaying the Federal advance would permit the Confederates to bring up reinforcements from Georgia and the Carolina's with which to strenghten the Army of the Potomac (CS) - it wasn't yet the Army of Northern Virginia - while also allowing for the procurement of more weapons and ammunition.
This meant that the Confederates at Richmond would grow stronger and be able to meet the Federals on near-parity, and this, indeed, would have been the case if Johnston had waited a couple more days before launching his offensive as the only forces that made up Lee's massive OTL Army during the Seven Days Battles that were not present in early June were Jackson's forces in the Valley.
Seven Pines/Fair Oaks was the first offensive Johnston had attempted during the war and pretty much everything went wrong, but before he fell wounded he was preparing to continue the offensive the next day. Most likely any chance for a decisive victory had been lost by the mistakes of the first day but the Confederate may have been able to win some kind of clear victory if Johnston had remained in charge since his replacements - G.W. Smith - was indecisive and not really physically or mentally suited for a field command and soon after suffered some kind of break-down but this is unlikely given that the Federals themselves reinforced the position and strenghened it.
Johnston would not lose his job due to the inconclusive battle. He had, to that date, conducted his army and its campaign well within the boundaries of what the authorities expected of him, and despite failure to win a decisive victory his army would not be weakened by it. Seven Pines/Fair Oaks would be seen as an attempt to take advantage of a fleeting opportunity, a risk worth taking but not one worth losing ones job over.
However Davis's confidence in Johnston would have been damaged even further - adding to the incident a few days earlier when he had come forward from Richmond to witness what should have been an attack at Mechanicsville by G.W. Smith's wing only to find nothing happening and not being able to find anyone who could tell him why - which might mean a closer level of scrutiny from Richmond into Johnston's conduct.
If Johnston is unable to drive McClellan away from Richmond with the enlarged Confederate Army then he will lose his job and be replaced, likely by Lee.
As for Robert E. Lee, he had offered to serve under Johnston in the AotP(CS) prior to Seven Pines/Fair Oaks because he was fed up with office work and wanted to be in the field. Johnston had turned him down because he was worried about Lee claiming all the credit for any victory like Beauregard had done after 1st Manassas/Bull Run, but after his unsuccessful attempt to defeat the Federals first time Johnston might be more receptive to the idea of Lee working with him - unlikely, but possible.
