Two points in response:
The whole point of Agnes' essay is to showcase an infinite regression problem: the basis for meaning in our lives can't rest solely on the existence of future generations, because in that case the fact that the universe is finite would force us to all become committed nihilists right now, today. Consider:
If life for the last generation is nothing but a horrifying, meaningless void leading to "complete ethical and political collapse", then surely life for the second-to-last generation would also be meaningless? (After all, who'd want to bring a child into such a brutal, chaotic, pointless world?) But if things are meaningless for the second-to-last generation, then by the same logic they would also be meaningless for the third-to-last generation, and so on, all the way back to us in the present day.
What you're looking for in response to this essay isn't a defense of altruism, it's a defense of any meaning or goals or values whatsoever (instead of just wallowing in nihilism). If I believed that all meaning in my life came from future generations, and then I read Agnes' essay, I might become depressed and nihilistic. But it's not just altruism that would lose its appeal -- everything would lose its appeal! If nothing matters, why bother making money, staying healthy, having fun, or doing anything? For some quality thoughts about nihilism, you might be interested in this short and entertaining post by Eliezer Yudkowsky.
Of course, if I knew the world was ending next week, that would be terrible news, and in light of that news it would obviously be foolish to continue with efforts intended to help the far future. So, to answer your question -- yes, if we knew for sure that the world was going to be obliterated very soon, there would be little point in trying to build anything or help anyone for the long-term. (There would still be plenty of point in helping others short-term, such as talking with friends and family and commiserating / consoling each other about the impending doom, and in enjoying the time that was left.)
Personally, although effective altruism is a big part of my life, I don't view "helping others" as a terminal value, something that's especially good and meaningful in itself. Helping others is good because it leads to good and meaningful things, like those other people living happy lives. Ultimately, I'd say that the foundation of "meaning" in our lives comes from experiencing our own subjective feelings, sensations, thoughts, and conscious awareness. My main goal in contributing to EA is to make sure that there are lots and lots of people in a thriving long-term future, so that they too can enjoy the wonder of consciousness.