I am using DESeq2 to analyse RNA seq data. I have 5 conditions each with two replicates and I am comparing these against controls again with 2 replicates.

However the issue is that one of control replicates was sequenced earlier. Thus only this control replicate belongs to a different batch from all other samples.

As suggested in the vignette I added batch in my design like ~batch+condition. However very few genes remain significant after doing this as compared to when do not add batch to design.

Is it recommended to add batch to design in such an experiment? Is there any other way to handle this scenario in a better manner?

That extra control sample isn't much of a help because the batches aren't balanced. As you can imagine, you won't know what part of the difference between the two control samples is batch related and what part is biological variability. With a balanced design, I'd always recommend adding batch, even if you just had a single condition sample in the batch. But here you might be better off not adding batch, such that variation among the control samples will be modeled as biological variability.