Jarin

You need to get two copies if you want both a lab entry and return science. That's not new, but I don't know what version it was implemented in.

Okay, this has come up in multiple threads in the past couple days, so I really feel like I need to weigh in. There's nothing wrong with regular mk1 cockpit for re-entry. I just went back and tested this, throwing some rapiers on my old panther SSTO (because there's no kill like overkill) 
flight album here


Aggressive direct re-entry from LKO

No problems.
I do shed my heat in orbit with a thermal control unit, but even that's not necessary. I tested again without heat-dumping and got a bit toastier on re-entry, but a bit of intentional tumbling shed enough heat to keep from anything going boom.
I had more issues with overheating going UP than coming back down. 3 rapiers on this is about 2.5 two many, I think.
 
The problem with what everyone's suggesting? You're spending too much time in the upper atmosphere. You don't need a higher PE, you need a lower one. Hit the thick air sooner, and you shed speed before you build up too much internal heat. If your PE is positive on re-entry, you're just slow-cooking yourself.

A pile of radially-attached SRBs.
Edit: To clarify, a stack of enough SRB to loft you sub-orbital, then stage those off, so you're left with several more SRBs and your passenger capsule. TWR 5+ means 5+ Gs, so you can estimate it in the VAB.

Okay, I loaded up the craft file in my sandbox save and blind-launched from the runway without entering the SPH.
Got it into orbit with 300m/s to spare, but dear god did it fight me for every inch. The simplest change I'd make to your design is less wing, and then give the wings you DO have some angle of incidence. Gvies you extra lift without having to angle the entire body so you have less drag. Once you have Big-S parts, you really want to minimize the use of old-style wings as much as possible. Unless you just really want that visual design, in which case you just over-engineer in the name of style. Still angle those wings a degree or two regardless, though.
You'll note in the picture above that I was actually short of LF rather than Ox, which is the reverse of what you want. Reducing drag should reduce the LF needed to get to orbit, which should help there, but you might still consider a Mk3 LF tank behind the cockpit.
Other minor tweaks:
-Move the tailfins out of the way of the engines.
-Get a radiator on that thing somewhere. Just one of the small deployable ones is all you need, but trust me, even if no heat bars are showing, that plane is still cooking there in that picture. If you only went one orbit and tried to land at KSC with it, you'd still have most of that internal heat and it would burn hard on the way down.
Non-tweak commentary:
I love the landing gear design. Even if it bounces awkwardly on the runway, it's got style.
 
Edit: Crud, I almost forgot to actually tell you the flight profile that got to orbit. Just run flat and level after take-off until you're in the 500-600m/s range, so your rapiers are at full thrust, before starting to climb. Then just keep yourself at about a 10-15 degree climb. You should continue accelerating all the way up, hitting 1300~ish before the engines start winding down. Adjust your climb rate accordingly. Watch that spedometer, and the instant the m/s stops climbing due to altitude, flip the engines. Then just set SAS to follow prograde until AP is in space.

With the severity of that turn, it really looks like the left engine nacelle is having its thrust blocked. This can happen even with symmetry, I've found. Try removing just the parts behind the engines and test-fly to see if it still has the problem (obviously this isn't a final solution, just troubleshooting).

If you can stay in physics range (25km in atmosphere, I think?) until it hits the ground, you're good. For everything else, look at something like FMRS. There's a 1.2 updated version in the last page or two of the thread. I've been using this for Virgin Galactic style high-altitude orbiter launches.
If you're just trying to get biome science info without landing, though, parachute drop-pods from a plane should do fine. Drop them low and circle if necessary.

I think I cribbed the mk2s-in-the-wing from @mk1980 (though his wasn't flipped vertical) but I've grown rather attached to it.
Anyway, here we go! The finalized Archon CTV (kerbalX link).
 
 
Full pictures and instructions below. 
Disclaimer: Pictures were taken across multiple flights, and there may be a couple design tweaks visible. However, all instructions are accurate for the final design.
Should be a pretty flexible design overall. I don't think anything but a couple RCS ports are attached to the crew cabin, so that should swap out for a cargo bay or whatever you need.