Should I ventilate a small waste pipe?
According to the International Plumbing Code, the length between a toilet (water closet) trap and the vent is unlimited. Which means if you're only installing a toilet, you don't need a vent.

International Plumbing Code 2012
Chapter 9 Vents
Section 909 Fixture Vents
909.1 Distance of trap from vent. Each fixture trap shall have a protecting vent located so that the slope and the developed length in the fixture drain from the trap weir to the vent fitting are within the requirements set forth in Table 909.1.
Exception: The developed length of the fixture drain from the trap weir to the vent fitting for self-siphoning fixtures, such as water closets, shall not be limited.

When you do install a vent for a plumbing system, the vent must terminate outside the building (and not within x distance of windows/doors/intakes/etc.). So there's no concern with smell, at least not inside the house.
As for the condensate drain. You'll have to check the manufacturers documentation, to determine if a trap is required. If a trap is required, you'll have to vent the trap. You'll determine the distance from the trap to the vent using Table 909.1



There's also the matter of drain size. The toilet should have at least a 3&quot; drain, and cannot lead into a drain that is smaller in size. So if the existing waste pipe that you're connecting to is smaller than the toilet drain pipe, you're going to have a problem.
It sounds like you're starting with a waste pipe simply sticking out of the ground.

To add the toilet, you'll want to connect to the existing pipe using a sanitary tee. You'll also have to maintain a proper slope of the toilet drain pipe.

I'd probably use another sanitary tee above the toilet connection, to connect the condensate drain to the waste pipe. Then cap the waste pipe.

If the manufacture of the boiler requires a trap on the condensate line, I'd probably use a trap and standpipe setup to connect the condensate to the waste pipe.

And if there's not a vent within the appropriate distance of the trap, you'll have to extend the waste pipe to provide a vent.

If you want to avoid the vent altogether, you could plumb the toilet as described above. Then simply have the condensate drain dump into the toilet. I'm not sure if this is an approved method, but it should get the job done.