First, I'll admit I'm a big proponent of day care because of what the kids learn there, especially as they get closer to school age. My husband was off work for quite a few months and we considered taking my daughter (who is almost three) out of day care, but both felt it was important enough to pay for and keep her there. Yesterday at day care they had music day and sang 'My Hair had a party last night' - there are a lot of things I wouldn't think about teaching her if I were to stay home with her. She also goes to Goddard.
I will tell you that we also had some horrible drop offs periodically - at 18 months I'm not sure he understands which days are school and which are not until you actually get there so that could be part of the problem (now we tell her before that school is tomorrow but I don't think we did it at that age). We had two things we did to make things work well as we arrived: 1) Get her there early enough so she is not overrun with other kids and can sit and eat snacks or breakfast quietly (this still works) and 2) Physically hand her to the teacher (this was more in the age range your son is at). Since I work at home frequently and can take her in whenever I want, I thought that keeping her later in the a.m. at home was better, but after talking to the teacher, we realized it was impacting her social bonding with the other kids. Now I take her in earlier, even though that's harder for me (I'd rather play with her more :)).
Oh and as far as the viruses, that's typical day care - now that my daughter is almost three (she has been in day care since around 6 months), she rarely has more than a slight runny nose sometimes. I think some has to do with the cleanliness of the day care and some is just the immune system (and they like to wash hands 'all by themselves' as they get older).
I think if you take him out and put him back in later, it will still be rough, but delaying it at this age wouldn't really hurt (in my opinion anyway). You just never know how a kid's mind is working - if he thinks he got you to take him out by his crying, he will cry more next time. But he might just get better in a few months.
Either way, good luck!!
S.