Howdy
45 Colt is not the best cartridge for the Winchester Model 1894. As you probably know, the 1894 was designed for a longer cartridge like the 30-30 or 32 Special and putting a shorter cartridge like 45 Colt into it is a bit of a compromise.
All that said, yes, you can load 45 Colt with Black Powder for any lever gun; with a caveat. Any lever gun is nothing more than a pipe. It is not like a revolver where fouling gets blasted out of the barrel/cylinder gap and gets everywhere. The trick in any lever gun is to chose a cartridge that will expand properly at the relatively low pressures developed by Black Powder to seal the chamber. If you don't seal the chamber, you will get blow back into the mechanism and will have to clean fouling out of the mechanism.
Many, many shooters in CAS load Black Powder for their various lever guns chambered for 45 Colt. 1894 Marlin, 1892 Winchester, 1873 Winchester, 1866 Winchester, 1860 Henry, and yes probably a few 1894 Winchesters. The common thread among all those shooters is that 45 Colt does not obdurate very well at Black Powder pressures to seal the chamber. This is because the case walls are relatively thick, around .012 thick at the case mouth. So what usually happens is they get some blowby into the mechanism that has to be cleaned up. Certainly not the end of the world, but it does have to be dealt with.
There are several strategies for dealing with this. First off, no light loads. You want to develop as much pressure as possible to completely seal the chamber. Use a heavy bullet like 250 grains, and fill the case with powder so that when the bullet is seated the powder is compressed by between 1/16" -1/8". No fillers, you want to develop as much pressure as possible to seal the chamber. And be sure you put a heavy crimp on the bullet.
Another trick that is used is to only size the case partway, so that the rear of the case remains in the expanded condition, better sealing the case. And some guys anneal their brass so it remains soft and seals the case better.
All this is why 44-40 is the darling of Black Powder lever gun shooters. The case is thinner, only about .007 thick at the case mouth, and seals the chamber better at the relatively low pressures developed by Black Powder.
Bottom line, go ahead and load up some BP loads with Black Powder, but be prepared to do some cleaning in the action.
And be sure you use a bullet with a Black Powder compatible bullet lube. Modern Smokeless bullets with modern hard lubes can be troublesome.