I think just about every motel you stay at in Branson can get you the two day for the price of one deal. SDC themselves also offers a deal where if you come after 3:00 p.m., the next day is free.
I'd second Lamburts; although, we always go to the one in Sikeston which I think is better. The hatchery is neat if you've never seen anything like it before but nothing special and doesn't take long to see. The Titanic is interesting if you've never done it before but very historical and museum like, not very hands on. I thought I'd really like it, but ended up getting a little bored with it. Silver Dollar City and College of the Ozarks are fun. There are also plenty of shows to see, my favorite was a Chinese acrobat show. Not sure if its still playing though as that was a few years ago that I saw it.
OP--DS also has food allergies (milk, egg, soy, pn, tn) and the throwing of the rolls is exactly why we won't go back to Lambert's. Terrifying to have food literally flying around that isn't safe for DS. They throw them from across the room--not just toss it from the table next to you. He doesn't eat restaurant food anyway (we always bring his food) but the thought of it terrifies me (and yes, I've been there so I know what it's like). We also don't take him to any hibachi style restaurants because of this same reason.
SDC has an allergy aware menu (info is on their website). We have never tried it before with DS. You can take you're own food into SDC, just like WDW.
If food allergies are a concern, I'd definitely avoid Lambert's . I've known quiet a few people to get hit with a stray roll when someone else missed. It's part of the fun, but not so much I imagine if you are allergic. They really do fly all over the room, over tables, over people's heads, etc.
Also, even if a member of your party chooses not to eat due to allergies, you'd still be charged for the pass-alongs. If you order, they are included with your meal. If you don't order, you are charged for them, even if you don't actually eat any of them. I think it's like $6 a person. You might be able to speak to a manager in an allergy situation, but not sure.
That's the other "different" thing about Lamberts - no doggy bags. So, last firm we ordered 2 meals and 2 pass arounds. Wanna say the pass arounds were $8.95.
They always say no doggy bags, but I've never not left without 2 or 3 to go boxes filled full. I've even had them offer them to us before filled with just pass alongs or with rolls. We didn't even ask. It's part of what I love about going there. I can usually eat off the leftovers for days. This is in Sikeston, though, so not sure if the policy is actually enforced at the other two locations or not.
We also went to Silver Dollar City and it was fun, but my kids actually liked the waterpark better. I don't remember the name but it was right on the main strip if i recall correctly. there are also several outlet malls if you like to shop and one had a Disney store when we were there. It was several years ago though.
One last thing, if you were married or born in 1976, you can get a free season pass this year to SDC.