Is this Obstruction.

At that age it's always a tough call. The runners need to instructed to run to the right of the bag for a couple of reasons: 1) Beacause first basepersons are still learning that it's not good to have your foot stepped on and maybe break it and 2) The running lane, after halfway and 3' wide is where they're required to run so the runners are not called for interference.
Your situation is not obstruction but had your runner attempted second base and was thrown out because the first baseperson interfered with his progress - that would be obstruction.