Adding an additional creature to the system isn't going to solve the cyanobacteria issue you are describing.
Cyanobacteria thrives in low flow areas and feeds off of excess nutrients in the water column. Water changes with ro
water will then address the nutrients in the water column.
As for the engineer goby's tunnels, they can break things down. The only issue could be seen would be if the rocks were placed on top of the sandbed to where it would fall down.