Daniel has always been a scientist, something they've had an unfortunate tendency to gloss over on the show. But they weren't showing us Daniel was a mad a scientist at heart--actually it wouldn't be the first time they've done if that was the case either.
In any case, Daniel has been a civilian member, a very trusted and high ranking civilian member of a top secret military organization. He has taken part in many dangerous military operations, more than some people in the military I dare say by this time, for many years now. He's used various guns(and with a good deal of proficiency), alien weaponry and even flown spaceships. Heck he's died, ascended and returned to life.
It is actually more likely they would send just Daniel and Dr. Lee, just a couple of scientists just going to the jungle to search for ancient ruins, than to send in a whole military operation which would attract alot of attention and the need to answer questions from a foreign government who would wonder why in the world the US military has such a big interest in something in their jungle. Even captured it looks to the Hondurans like it is simply a matter of concern for kidnapped citizens.
Actually a couple years ago Ewan McGregor did a Jungle survival special with Ray Mears, the survival expert in Honduras, where they visited archaeologist Dr Chris Begley, from the University of Kentucky who was digging some very obscure culture knows as the Prehistoric People of the Mosquito Coast in caves of the rain forest--so it actually isn't as "far-fetched" as some of you may be thinking.
Most likely the reason it was done that way was because it allowed for a good cover story both to explain their being there and also in the event anything happened.
It is one of the few times we got to see Daniel doing his "thing" on Earth. The Curse was different, it was pretty much all in Chicago and then a brief sojourn to a sandy land supposed to be Egypt and it was more a murder mystery involving the goa'uld. We got a good contrast between the nervous Dr Lee and Daniel, who wasn't at all worried over whether their guide would be there, knowing they'd find another if he wasn't by "having a few beers and making a few friends", which leads one to think he'd dealt with such a problem before on exploratory digs. He was focused. I could imagine what he'd have been like on one of his own digs back when he used to do that stuff.
As for the rest of the episode, I actually liked the supersoldier--a little too much of the slow-mo but I thought he was fairly creepy. I liked that part of the episode as well, though I liked the jungle part better.
