Truman believed use of the atomic bombs would save the lives of more than 100,000 U.S. soldiers. Despite the horrific devastation of the first atomic bomb drop, Japan refused to surrender. Truman was advised that continued ground fighting would cost more lives on both sides. He felt atomic weapons were the best strategic decision.
While the petition reaching Truman prior to the bombings may have resulted in some reconsideration, I do not believe that a petition to delay using atomic weapons on Japan would have swayed Truman. The political climate at the time was far too volatile. While those working on the project would have a had an advanced scientific understanding of the immense destruction and horror that would occur, I do not believe their concerns would have been regarded as relevant from those looking at the situation from a merely political standpoint.
The US purposefully dropped the atomic bombs on cities that had been largely untouched. Tokyo, Kobe and Osaka were pretty much destroyed by American fire bombings already. It was especially brutal because Japanese cities were mainly built out of wood. He did it twice (Hiroshima and Nagasaki) so I think he was okay with it.
President Truman was well-versed at the level of destruction and death that the atomic bombs would cause in Japan. He also knew that there would be many that would express moral outrage and conscientious objection when the extent of the damage was known, which is why reporting of the atrocity was restricted. Therefore pleas from scientists would have been unlikely to have swayed him.