We started using Trifexis this year too and I've been really happy with it. No adverse reactions and no problems with fleas since using it. Plus its really convenient that it treats heartworm too.
My vet too recommended giving it to them with food.
My vet is against the use of the majority of the topicals, there's only a select few that she recommends. Trifexis being one of them. She feels that the chemicals in many topicals are just too toxic.
I did do some research online about Trifexis. The fact of the matter is, there are horror stories and the potential for an adverse reaction with every drug. You just have to look at your dog/situation and weigh out your options.
What I found in my reading was that the 'reactions' that people documented were exactly what the drug warns about in its facts sheet and almost never resulted in deaths. Deaths only seemed to occur in dogs that were not well in the first place and the drug company did not experience any deaths in their testing, unlike with some other topicals.
I also noticed that people were still giving their dogs the drug after they'd experienced an adverse reaction, which is just not using common sense.