I am divorced and remarried, with a son from my first marriage and a daughter and son from my second. My ex has also remarried and has 2 daughters with his wife. Our son goes back and forth, and spends 50% of his time with each family, so our somewhat situation is different than yours. I have to say this -- it's difficult to accept step parents as part of your child's family when you haven't chosen them... much harder than the stepparents that you do choose, but like it or not, they are part of your son's family. Let them take a picture. Even if your son hasn't seen very much of them, they are his family. Your son will know who has raised him, who sits with him when he has nightmares, who takes care of him when he's sick, who celebrates his accomplishments with him, etc. He will also probably love his father, and miss him, and really like having these pictures. You probably have family who you don't see often -- not more than once or twice a year -- that you care about. Isn't it nice to have pictures with them? It's hard, but you should encourage your son to have a relationship with his dad, and yes, with his stepmom. He needs that connection.
My son has pictures with just him, me, and his dad. He also has pictures with each family, formal and informal, as well as pictures of him with any one of his 4 parental figures. Each family is a family, and he feels lucky that he has so many adults who care so much about him. When he tells us he wants it, he even gets the occasional dinner out with just his biological parents. Now, we've worked very hard to get to the point that we can work easily together and it's really not a big deal to interact in a friendly way at this point. My son is also almost 10. It might confuse a 5 year old -- I don't know. Depends on your son. My point it, this needs to be all about what's best for your son, not what's best for you. When we have kids, we have to be grownups about divorce, and make sure that their needs and best interests take top priority. I know it's hard -- there were (and are, when I'm honest with myself) so very many times when I selfishly wish I could have just gone for the every-other-weekend-with-Dad model, because there is nothing I would like more than to have my son with us most of the time, but then I see how very happy he is, and how he has a great, close relationship with all of us, and this huge support network, and I'm sure that it's all worth it.
Sorry for wandering off the point for a bit - I need to tell myself that occasionally -- particularly when I start feeling selfish again :-)
Anyway, I think that the picture with his dad and stepmom is a perfectly fine idea, as is pictures of him with his dad to be framed and put in a prominent place in his room. And, perhaps, encouraging frequent phone calls if seeing his Dad frequently is not an option. Only you would really know if the picture of the two of you with him would confuse him or not. Perhaps that ought to wait until he's older. You don't want him to think that the two of you might get back together.