Welcome although I am sorry you found a need to be here. The parents here are an excellent source of information, advice, and encouragement.
EEN was great for my daughter. We used it instead of adding Methotrexate when Remicade wasn't quite getting her to remission. EEN has proven to be just as successful as prednisone with getting some kids to remission. THe added benefit is good nutrition and help with weight gain etc. However, it only works while you are on it. Once stopped, the disease creeps back. For some it is a few weeks, some a few months. The problem is that while disease is creeping back in it is doing damage. For this reason most docs will use EEN the same way they would steroids.
Most maintenance meds take a while to get to therapeutic levels. For this reason docs usually start the maintenance med at the same time as prednisone or EEN. The hope is that by the time you are fully tapered or have completed the 6-8 weeks of EEN the maintenance med is ready to take over.
I know the risks are very scary at first. But the risk of undertreated or untreated disease are even worse. Here is a very helpful presentation on risks that helped me make all of our med choices. Believe it or not, my daughter has been on these meds for almost three years and been doing amazingly well but I still have to read this from time to time to reassure myself.
http://www.ccfa.org/assets/pdfs/risk-and-benefits-transcript.pdf
BTW - as for their risk of catching anything, my daughter is the healthiest one in the house. We have had the flu, mono, colds, stomach bugs etc all brought into the house and she is the only one who has escaped unscathed every time. As a matter of fact, her youth group was on a trip and of 13 of them 7 came down with mono...go figure.
Good luck with your decisions.