You're right. But as you said, DPS is an average, and saying 1k DPS is implying 1000 damage in one second, whether that is the truth of the numbers or not, that is the implication. Over the span of those two seconds, you did 2k damage, which as an average, is 1k a second. Obviously because of the nature of the abilities you used, that's not the actual damage ouput, but when you average it out, it is.