I don't think that you can generalize your way to a predictable rule about how a new acronym will be pronounced—in part because a lot of factors—some of them quit unpredictable—are in play.
One strong influence, as both you and Alison Hunt recognize, relates to existing words that are spelled the same or similarly. This influence can actually pull in two different directions: toward adopting the same pronunciation (as happens when people pronounce WAR identically to war), and away from the matching sound (as happens when people pronounce WAR to rhyme with far).
The arguments on both sides are not entirely unreasonable either: Adopting the existing pronunciation means not introducing yet another "new word" to the world; but on the other hand a different pronunciation avoids confusion in a world where the established word is much more likely to be assumed in the absence of a special explanation.
But looking a random sample of acronyms, I don't see much evidence that the way a letter in an acronym is pronounced in the word it comes from influences the way the acronym is pronounced. Consider these three examples: FEMA, SCSI, and URL.
FEMA is the abbreviated name of the Federal Emergency Management Agency, and the E in the acronym is indeed pronounced like the E in Emergency; but the A in the acronym does not match the pronunciation of the A in Agency. If original letter sounds determined pronunciation, we would expect FEMA to be pronounced "feemay"—but it isn't.
SCSI is the abbreviation for the Small Computer System Interface, so a strict adherence to the sound of the represented letters in the acronym would be something like "sksih"; but because tech people loved the idea of saying "scuzzy" all the time, that's the pronunciation that stuck.
And finally URL, for uniform resource locator, is sometimes pronounced as an initialism ("U-R-L") and sometimes as an acronym that rhymes with the aristocratic noun earl. It appears that very few people consistently pronounce it "yoorl."
The situation with WAR is not yet settled, and I have heard people use the rhymes-with-far pronunciation. If that's the pronunciation that you would like to see win out, then by all means use it that way yourself—the more frequently (and persuasively), the better. But I wouldn't recommend appealing to the original letter-sound pronunciations of the acronym to bolster your advocacy, because there just isn't any there there.