This is an interesting thread. TL:DR; This change is positive, in my opinion.
First I would note that although WotC have de-emphasised alignment ( so "good" vs "evil" should be less of a focus ), Larian did initially ask us to try out the "evil" path. Since the major discriminating decisions we can make comprise those accepting or rejecting the "help" of the Illithid tadpole, it is reasonable to link those to good and evil, at least in a general sense.
In the situation we are roleplaying, however, I would not consider it immediately obvious that employing the tadpole while on the Nautiloid has any particular implications. Until you understand something, it is difficult to characterize it, so using the tadpole to interface with local Nautiloid systems, would not necessarily, and obvioulsly, be "evil".
While all characters would, in principle, be likely to recoil from any path that seems to interact with the "thing" placed in their skull ( whether or not characters are familiar with Illithids and their tadpoles ), does that override all other considerations of "good" and "evil"?
In particular, with Shadowheart in the Nautiloid, you are faced with the choice of releasing a fellow-victim, or probably consigning her to death. Ignoring all foreshadowed knowledge you now have about how the game plays ( which may not actually be true of the released game anyway ), I would argue that releasing SH, regardless of the cost to yourself, is unambiguously a "good" act.
In my mind, a paragon of "good" would not hesitate in this decision, and would selflessly choose to release SH. A "neutral" or "evil" character would balance the extra ally against the risk they perceive to themselves. It is a pure role-play decision, but one that greatly favours a player releasing SH, and thereby introducing the player to what may be the game's most important story mechanic, without any real in-game consequences.
As far as EA goes ( which may not remain true in the released game ), the continued use of the tadpole, and the consequences during long rests, advance a player's understanding of both story elements and personal risk. There is frequent, and ample, opportunity over time to understand that you are trading advantage ( power ) for disadvantage ( subservience ), and when approaching a point of no-return, you are left in no doubt, as there is a dialog that tells you that using the tadpole again will change you.
In EA this seems to do nothing other than change the "[ILLITHID]{WISDOM]" tag on auto-succeed dialog options to a "[TRUE SOUL]" tag, but I haven't played through as a True Soul often enough ( or recently enough ) to know if I have missed changed behaviour. But, I would be surprised ( and very disappointed ) if the released game did not play very differently depending upon this decision.
You are right that using the tadpole itself is not inherently good or evil. The action you undertake utilizing it would be what might be considered good/evil.
My problem is it seems to me that Larian is designing things under the assumption that most players can/should use the tadpole at least some bit. Like you said they let you know about that potential point of no return. While the average person indeed probably doesn't have a lot of knowledge about mindflayers and tadpoles, that tadpole insertion was intense and I just can't see most anyone thinking it would be a good idea to mess with it further. Also Gith are not the only race who are familiar with flayers and have a long history with them. Drow and Deep Gnomes at a minimum would quite probably have an understanding of what just happened as their races interacted with and/or were enslaved by flayers for hundreds of years. Regardless of the "special-ness" of this tadpole I don't see one of those 3 races touching it with a 10 foot pole, but I haven't seen any racial differences in the tadpole interactions.
