According to numbers I found, an "average" bulldozer burns 4 gallons of diesel an hour, yielding an annual emission rate of around 66 tons. Let's assume for sake of easy math that other earthmoving equipment has a comparable enough emission rate that we can just call it the same. If it takes 10000 pieces of earthmoving equipment 10 years to dig a canal (a complete wild-assed guess, admittedly), that works out to 6.6 million tons of CO₂.
Per my previous comment, we'd established a long-way extra emissions rate of ~20000 tons (19.6k metric tons is 19.9 and small change thousand long tons; call it 20k for easy math) per ship, per trip.
Remember that, to calculate whether the canal is a "clear winner" in terms of emissions, we have to compare the emissions saved by ships using the canal, not the extra burned by ships that don't. At 17 and a half thousand ships in 2015, saving 20000 tons of emissions each, that's 350 million tons in 2015 alone — over fifty times our estimate of the emissions from constructing the canal.
Yes, it's WAG envelope math, but even if we up the estimate by an order of magnitude — 100000 pieces of equipment over 10 years, or 10000 pieces over 100 years, or however you want to factor it out — that's still a five-fold win, in just one year. On a canal that's been in operation for some 150 years.
So, yeah. Unless someone can offer better numbers than I have, I'm going to run with "clear winner", thanks.
All that aside, I'm not even going to attempt to rebut to your naïve optimism over technology and good ol' Team Humanity's problem-solving spirit coming along to save the day, or your blasé "Extinctions, shmextinctions" tone. They're, IMO, premised on beliefs so divergent from reality, they don't even warrant the effort.