Yes, you can use DESeq2 for allelic imbalance. We've used this in two papers, and the AI results were in agreement with QTL analysis that uses an independent type of data to find imbalance. The basic design is ~sample + allele.
You can also test for differential AI with an interaction between the allelic effect and the condition. You'd need to use the strategy outlined in the vignette (condition effect within samples, but comparing across groups where samples are nested within groups).
Just to note, we've also developed the Swish method (in the fishpond) to allow for various allelic expression designs. But you would need to quantify allelic expression with Salmon and have bootstrap replicates for that method. We will be posting more about this soon, but you can already see the fishpond devel branch for details.