Unfortunately, Misfit cannot open Half-Life MDLs directly. To be fair, either can Milkshape.
As far as I can tell, Half-Life models are a compiled format. They contain the skin graphic, the different LOD models and the animation data in separate files within a container file of some sort (the MDL). Even Milkshape, which had as one of its main purposes the ability to work with HL models, needs to decompile them before it can work with them.
Milkshape can, of course do that...

...and then you can "import" the mesh into the editor. Note that I do say "import". You don't open the file; you import it into an existing model. The existing model can be a completely blank one and it feels just like opening it but it isn't. One very important difference is that the animation doesn't get imported, only the basic mesh. You can then import the animation but it is a bit flakey and I have had major problems with Milkshape animation. MD2 and MD3 models also cannot be opened, only imported, and there is no way to import their animations into Milkshape. So if you import an MD2/3 into Milkshape you only get an unanimated mesh to work with.
Saving an MD3 in Milkshape is also tricky. You don't "save" an MD3, you "export" it. To do this you need to generate the control "QC" file (Milkshape has a tool for this) and then export the MD3.
From memory, MD2s have a hoop or two to jump through as well.
By contrast, Misfit handles the file types that it knows very easily. Most files can simply be opened/saved (you specify which file type you want by typing the file extension (e.g. MD3) with the file name as you save it. Misfit recognises this and saves the file appropriately; a nice, easy, quick conversion. It also preserves animations so if your MD2 or MD3 was animated, it still will be provided you save to a format that can handles frame-by-frame animations.
Open:
Save:
Like I said though, it doesn't handle HL models and although I've had more success with its animation system, it is also known to have problems.
The reason that none of the models sourced from HL in the original Paranoid release were animated was because of the difficulty (read impossibility for me) in getting the animation to work using these tools. I have no idea how to perform any of these tasks in Blender or a big commercial package like 3D Studio or Cinema 4D but perhaps they could be better.
Milkshape and Misfit are cheap/free little tools and are (for the most part) about as easy and approachable as it is possible to make 3D low-poly model editing (still not
that approachable) whereas Blender is a very complicated, very comprehensive program with the UI from hell. I understand that once you master it, you can make it do many, many things though. 3DS is very powerful. I used to have a (free but legal) copy and things like the animation and so on worked pretty well and the UI was much better than blender. However, I changed computers and the copy I had was an "on the machine you install it on only" offer and I had never really got to grips with it fully anyway. As a result, I tend to stick to Milkshape and Misfit (and very occasionally Blender for some specific tasks). Basically, I use nice, quick, easy tools that I know how to use quite well and which allow me to do do most of the editing that I need. People like Willem Sitters or LilWhiteMouse are far more adept at creating and working with models than I will ever be.
There is, however, one more program that I haven't mentioned:
Noesis. It has some very powerful features which I certainly under-use. It isn't an editor. It's a model viewer and converter. It isn't immediately obvious but it has some very powerful conversion features that allowed me to, for example, grab some of the models from Jedi Outcast and convert them to MD3 files with their original animations.
e.g.
I don't know how well (or even if) it supports the native Half-Life format.
BTW, here are a couple of pictures showing the lack of precision that can happen with MD2 versus MD3. The model is the Ravenclaw space ship from Jedi Outcast...
'''and the pictures specifically look at the precision of the jet engines on the side.
The original model converts well to an MD3 (it may even be an MD3 in the game; some models are but there are a couple of other formats used too).
However, convert it to an MD2 and the accuracy required for the nice precise pointy bits in the engine simply isn't there at the resolution of this model.
[voice of bitter experience]Note, the lack of precision happens because of the change to MD2 format. Unless you reload your file to see what the MD2 looks like, you'll still have the working version open which may not show the inaccuracies so you may be unaware that you have screwed your model until you look at it elsewhere.[/voice of bitter experience]
Now, imagine what those inaccuracies look like in an animated model where the rounding of coordinates can be slightly different in each frame. The model would seem to wobble - sometimes really badly. This isn't too much of an issue if the model is meant to be a living creature but if it's something very fixed and solid like a machine it looks terrible. e.g. I once made a model of a machine that was essentially just a complicated looking box with a rotating wheel on the side. The only bit that was meant to move was the wheel. However, when I animated it and then exported it to an MD2, the box part wobbled around making the whole thing look ridiculous.
Some of the lack off accuracy
might be down to the conversion tool used but even MD2 models produced by expert modellers on expensive software can show such wobbles (e.g. if you look closely at some of Willem Sitters' Doom enemy models you can see a bit of wobbling going on and wobbles are certainly present in all the Strogg from QuakeII) .