Without getting into the moral or religious corners of this discussion - I wonder how long it’ll be before we create something we can’t contain.
I've genetically engineered E. coli hundreds of times, and I've never caused a gene to be integrated into the chromosome. I usually put the gene into a plasmid, which I force the bacteria to use by also growing them with an antibiotic; if they don't have the plasmid, they die. I guess that integrating genes into their chromosome would obviate the need for using antibiotic, which might be important for industrial scale processes. But for the ordinary bench scientist, I think plasmids are going to remain the gene delivery vehicle of choice for a long time.