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Yes, the canoes can carry people. (In spite of the fact that they look like one man kayaks. The graphics for this will be changed in the next version after 0.3 and an actual kayak unit has been added, which acts as a scout and doesn't get bad results from the "goody islands".)
It also didn't actually hurt much as the hunter unit has a large built-in bonus vs. these animal units and also has two hunter promotions which give another +100% or so, and is on a hill with jungle for another 75% defensive bonus so his effective defensive strength was probably something up close to 15. He pretty well cleared them out, capturing some of them and killing the rest for food and production, if I recall correctly.
If it crashes immediately without ever getting to the menu or spending a noticeable amount of time loading it sounds like a version issue. You must have BtS patched to version 3.19 (the last version).
The installation instructions have been updated as it was finally noticed that the name of the folder in the 7-zip archive is not what it was supposed to be.
It is the Final Frontier mod that comes with BtS, or a mod-mod based on it.
There doesn't appear to be mod-mod of FF here on ModDB, but there are a number available elsewhere including Final Frontier Plus which fixes the known bugs (there are significant bugs in regular FF) and expands it some.