Is it possible to use DESeq2 for transposon insertion sequencing analysis?

The experiment is to construct a library of transposon-insertion mutants and compare the relative quantity of mutants before and after experimental condition. Since the transposon is supposed to disrupt the gene function, enriched mutants after this selection suggests the gene is deleterious for this process and vice versa. 

After getting the read counts for each possible insertion sites/genes for different samples, conceptually can I use the DESeq2 package for differential analysis between different conditions/time series? 

It sounds reasonable. DESeq2 can be used to compare tables of overdispersed counts in general. Each library will be robustly scaled to account for sequencing depth, as with standard RNA-seq.