Sorry, no medal. A structural engineer will see only his part of the work, while an architect has a full overview of the entire project, including the structure.
Maybe those joists would have a prayer of holding if significant steel bracing were applied to them, and by that I mean hot-rolled steel angles as big as the pipe will allow, on all four corners of the joists, extending from support to support. Anything less than that is wishful thinking. The angles will have to be engineered before any installation is attempted.
Failing that, the only cure would be to remove the piping, sister the joists with new joists of the same size extending from support to support, and reroute the piping below the joists, or redesign the layout so that the piping runs parallel to the joists. Both the plumber and the general contractor should have known better than to try such a stunt. No matter how much plywood you stick on the sides, it ain’t gonna help.