Okay, so I found the source of confusion, the reciprocal of r is called \alpha.
So DESeq2 reports this \alpha. I guess zero dispersion suggests that variance and mean are same that is \mu = \sigma^2. So it is no longer a negative binomial distribution. A possible hack I can think of is putting a very small value to navigate divide by zero overflow. Please suggest if there is a better way.
The variance can then be written m + m2/r. Some authors prefer to set α = 1/r, and express the variance as m + α m2. In this context, and depending on the author, either the parameter r or its reciprocal α is referred to as the “dispersion parameter”, “shape parameter” or “clustering coefficient”, or the “heterogeneity” or “aggregation” parameter. The term “aggregation” is particularly used in ecology when describing counts of individual organisms. Decrease of the aggregation parameter r towards zero corresponds to increasing aggregation of the organisms; increase of r towards infinity corresponds to absence of aggregation, as can be described by Poisson regression.