When Lee surrendered, the Civil War wasn't over yet, he only surrendered the Army of Northern Virginia. As to why he did that, it was probably because his army was on the brink of total dissolution, and Grant offered him a way to save the life of his remaining soldiers.
The army of Northern Virginia was in really bad situation on the 9th of April, they lost a lot of men in previous engagements, and soldiers deserted en masse. The remaining army was cut off from supplies, and the road was blocked behind and before them by strong enemy forces. The last rations with the army have been issued previous night, and some troops have been starving for days.
In such situation you can do four things:
try to break through the enemy, and elude them
let your men go in small groups, so some may slip away
dig in and wait for the enemy to starve you out
surrender
A breakthrough has been attempted in the morning, but it failed, and there was no reason to think that a second attempt would fare better.
Trying to slip away in small groups would have ended the Army of Northern Virginia as an effective fighting force, they would have to leave behind their artillery, and a lot of people would probably just go home, as most of the soldiers lived in the region. The rest would be hunted by an overwhelming enemy force, while they would have to live from the land.
Staying where he was, Lee would have been starved out in a matter of days.
Surrendering meanwhile was a good option in this case, because Grant offered generous terms, and in the end he even allowed the rebel soldiers to keep the horses and mules of the army, and take them home.
As for the guerilla war, Lee actually expected the war to continue for a while, he said so much to Grant, according to Grant's own memoirs. The exact sentence is:
"Lee said to me that the South was a big country and that we might have to march over it three or four times before the war entirely ended, but that we would now be able to do it as they could no longer resist us."
So Lee expected some low-level resistance to continue against the Union. As to why it did not happen, I am not qualified to answer that.