If Martinez isn't going to get an overall result, of course you'll have Lebrun as teamcaptain in the next stage.
You are right, but in my mind it is not easy. Of course, that has everything to with my own mind.

Because Martinez will be the teamcaptain in stage 4 anyway, and by being also the teamcaptain in stage 3, he might score a few GC points.
Lebrun is not a hill sprinter, and as teamcaptain in stage 3 he might score less stage points as Martinez might score as GC points.
And some other things play a role too. For example weather icons, and the fact that I love to compete in the GC.
But on the other side, Martinez will be sold soon, so I don't have to consider an eventual Colombian individual championship.
Even stage 5 plays a role in the strategic decision of stage 3. Most likely Portugal will get support to go for a top stage 5 result.
If I could predict/estimate the GC chances of Martinez better, it would be easy.
This horrible stage 2 with an unexpected very big time loss, makes this strategic choice difficult.