I like to fly the squid occasionally, to toy around, but I barely ever pick it when I encounter serious opponents. While it's possible to stay out of enemies lines of fires in most CQC situations, it's very hard to bring two guns into arc at the same time and at the end of the day the squid simply lacks damage output. Currently I can't think of a Team Setup where the role of the squid can't be better fulfilled by another ship. The squid needs a little boost to become a viable choice for tough encounters.
As a possible approach, turning the side gun to the front popped into my mind as well. However I agree with those who say that a 45° side gun would ruin the flight style of the squid. What about turning the gun roughly 10° to the front (so the angle between front gun and side guns is 80° instead of 90°). That way maintaining a bifecta at the front would be significantly easier for a wide range of weapons which would ultimately result in more bang for bug when choosing the squid.
The rear gun could be turned slightly as well to still allow a 90° rear bifecta.