Back in the 1970s, a scientist named Ananda Chakrabarty received the first patent for a genetically modified lifeform, an oil eating "Superbug" from the bacterial strain Pseudomonas putida. The feat was doubly hailed as a major step in bioremediation and a travesty of nature. In the long run, Chakrabarty's Superbug was a failure. It was unable to survive in the wild, unable to compete with native bacteria, and unable to move towards food sources.
The moral of the story is that it is very difficult to tinker with nature and produce an organism that can survive outside the rarefied confines of the laboratory. It takes a certain amount of hubris to believe that we can outdo 4 billion years of natural selection.
Genetic engineering? Nature does it all the time. Scientists call it horizontal gene transfer.
Bacteria can share antibiotic resistance genes. Viruses often encode virulence factors that make bacteria make you sick. Among eukaryotes, examples of horizontal gene transfer are popping up every day among organisms as diverse as plants, nematodes, beetles, and yeast. Even human--gasp--may be riddled with the remnants of horizontal gene transfers: transposons, "jumping genes", retroviruses, B chromosomes, even our organelles.
Engineering life is as old as life itself. We may be the first to do so in a conscious directed manner, but let's not kid ourselves into thinking we are the first. There is no doubt there will be mistakes made along the way, but fears of Frankenstein fauna overwhelming nature are vastly overstated. Genetic engineering has already overwhelmingly benefited our lives in ways that most of us are unaware of. Simply put, the benefits have outweighed the costs by several orders of magnitude.
Chakrabarty, A M; Mylroie, J R; Friello, D A & Vacca, J G (1975), "Transformation of Pseudomonas putida and Escherichia coli with plasmid-linked drug-resistance factor DNA.", Proc. Natl. Acad. Sci. U.S.A. 72 (9): 3647-51, 1975 Sep, PMID:1103151
A major problem with oil-eating bacteria is that oil is not a complete diet. To use them to clean up an oil spill means providing nitrogen, phosphorus, etc.; whatever is lacking in the oil. Probably do more harm to the ecosystem than the oil spill did.