To Had or not to Had

When I first published Optimus: Praetorian Guard my wife proofread it and since she's an assistant editor of a state religious weekly paper and spent thirty years doing nothing but proofreading I was reasonably content with it being grammatically correct.
When I started attending writer's workshops I bought a book by one of the local authors entitled: Revising Fiction Making sense of the Madness. When Kirk Hickman was plugging his book and trying to get us to attend his workshop he offered one piece of free advice. "After you're through writing for the day go back over it and delete every 'had' that is not needed."
I was reading a book at the time which was really good except it read slow and  would get bogged down. I thought I was losing my ability to concentrate and was a little worried.
After hearing this advice a light bulb went off. Here are some examples from A Week in the Life of Corinth by Ben Witherington III with my corrections.
The captain had offered the morning sacrifice.
Niconor had seen enough sea voyages for a while. His poor stomach felt like it had swallowed half the Adriatic Sea, which he had just crossed on his way back from Roma. He had fallen (fell) into a pattern of only eating later in the day from the stock of dried fish he had brought with him from Roma.
That's just the first two paragraphs. Only in one sentence the use of past perfect tense didn't bog down the reader.
When I purchased the publishing rights to Optimus and started editing and revising it to release as an e-book the first thing I did was get rid of all those unneeded "had" this and "had" that.
I revised a number of my other novels, the beauty of e-publishing letting you repost after cleaning up your mistakes. I find myself after I had just finished writing something that I had thought was the best stuff I've ever written having to go going back and getting rid of the writer's form of space filler, the dreaded superfluous "had."
The point here is that grammatically those sentences are correct and editors of major publishing houses give author's the liberty of using this style, but if you want your work to read smoothly and easily take out the linguistic speed bumps.