In regards to consuming Aegis, consider this; Who would be the greatest threat to the Hero once they become a Fleshweaver?
Aegis is not especially knowledgeable in regards to the intricacies of soulweaving, having only been a young Soulweaver at the time of his death; he even states that he only 'did what I was told'. If Secundus had approached a spirit with the knowledge of Danyel, the phrase 'flesh is my thing' would have set off alarm bells instantly. Even Lanrete would recognize that Secundus is the spirit of a Murk.
As long as Secundus can keep Aegis either confused or in the dark, he might consent to the Hero being a Fleshweaver. However, if the Hero became one while he was still in existence, he'd see firsthand what-- exactly-- Fleshweavers are. This is likely true of most soulallies, but something tells me a spirit of Valour wouldn't be too pleased with what the Hero had become.
Additionally, Aegis is a spirit of defence; given the propensity of corrupted spirits to consume weaker souls, and his emotion being to protect the weak, there's a high probability that he can shield spirits from being consumed.
He might potentially kill the Hero before we acquired too much power.
So, essentially, I suspect that Secundus has Fleshweavers consume their soulallies because it eliminates the greatest threat early-on. Well, being the spirit of
cowardice Duality he probably has two reasons; the other being that it's preferable to have a bond with a creature you're going to assimilate into your body.