If I understand correctly you want to associate transcription rate with the read counts after ChIP-seq from PolII Ser5/2 phosphorylation. I think this will not give you the desired results because:

1. Elongating Poll II speed is not constant and may even stop at some positions, which in turn translates into higher read counts at those positions.
2. Gene length inversely correlates with the amount of elongating PolII. Larger genes have on average less PolII over the gene body
3. Regions at overlapping genes have a mixture of Pol II signals, one for each gene.
4. Elongating PollII creates broad peaks over the gene body that require a higher depth of sequencing to accurately identify them. MACS can miss many elongating PolII broad peaks when few reads are used.

I don't think you need to call peaks in this case because, as you say, any enrichment will be found at gene bodies. Rather you can try to get an average of the PolII (preferable the log of chip vs. input) over the gene body of all the annotated genes and try to cluster those values. At least you should be able to distinguish active vs. inactive genes. To measure transcription rates the method commonly used is GRO-seq.