I am in the middle of splitting cases on a 79 dt175 that has a blown top end and the crank and connecting rod have rust from sitting. I am wondering how easy it will be to clean up and be usable and how you guys would recommend going about that? 

It really depends how bad the rust is and where it is.
If it just surface rust it can be easily cleaned up with a wire brush and maybe some rust converter. However if the rust is on the oil seal areas that could cause an oil leak, once again depending how bad the rust is.
As long as the big and small ends are up to specifications it would be fine to use.

If the rod or main bearings rusted, they will fail very quickly.

I've never done it--but-- if the crank was separated could you have then bead blasted to bring them up like new. & as MarkT says, if the rod or mains are rusted--its downhill from here on.

The rust appears to be surface rust and I don't think it will be too bad to remove. I will post some pictures when I get the chance. I will investigate the main bearings when I get back in the garage as well... hopefully, they are all good. Should be able to get pictures up soon.

Here’s what it looks like 

Here's my view for what it's worth.
Con rod kit £31.50.
Crank rebuild £45.
I think I paid around £60 for all the bearings and seals.
These are the prices I paid last year (in the U.K.) for my CT3 bottom end.
For less than £140 you could rest or ride in the knowledge that your engine is the best you can make it and isn't going to let go and cause more cost.
As I said, just my view.

Just curious is the surface rust on the crank weights the concern or what's unseen inside the rod connection? 

if I could see any rust or feel any roughness or excessive play in big end after washing it out real good with BBQ lighter fluid, then I would rebuild crank.  Same with other bearings too.  If bearings are are clean, tight and super smooth then reuse, if not bite the bullet and avoid having to take engine out and apart again vs. go for a ride, or worse have wife ask if are you sure know what your doing 

My concern is big end rod bearing. One tiny speck of rust in there and it will fail quickly. No matter how smooth it feels. 

Often the bearing is pretty oiled up so could be fine. Just look for rust in there. Rebuild is safest of course.