Its your DM's call.
When the rules are ambiguous, it is up to the DM to adjudicate.
If you disagree with the DM's decision here, you can discuss it with them and try to come to a new agreement about what your class restrictions mean, or ask to be allowed to rebuild if the character you initially envisioned doesn't work under their interpretation of the rules.
Your DM's decision is well supported by the rules
The prohibition against being a shadow weave user doesn't care how you get your shadow weave magic. If it meant only to ban the Shadow Weave Magic feat, it would say so. A someone who uses the shadow weave is a user of the shadow weave, no matter how they got access to it.
The prohibition also doesn't care about who the target of your shadow weave magic is. A reformed shadow weave user turned follower of Mystra who has sworn off the shadow weave magic except when fighting other shadow weave users might well be an interesting character, but that character doesn't qualify for the Knight of the Weave prestige class.
A spellthief who uses stolen shadow weave magic against its original casters is still a shadow weave user - just one who got access to the shadow weave through nonstandard means. Mystra would prefer that those spells not be cast at all.
On a technicality, you might be able keep your powers, if your DM accepts it
Unless otherwise stated, you do not lose access to a prestige class's abilities just by failing to meet its prerequisites, and indeed, can even continue to take levels in it.
There are no rules that say a Knight of the Weave loses their powers if go against the principles of the class, unlike Paladins, Druids, and many prestige classes from the Book of Exalted Deeds. Thus, RAW technically allows for Knights of the Weave to use their abilities however they like after initiating into the class. This includes becoming a Shadow Weave user.
Thus, an oathbreaking Knight of the Weave can continue to use their powers and even continue to take levels in the class.
That said, I do not recommend making this technicality in the rules as the basis of your argument. When discussing rules with your table, you should advocate for what rules best serve the game you all want to play, and explain why your interpretation better fits that than another interpretation. There are no RAW police who will slap your DM's hand or take away their cookies if you try to argue this technicality and they say "No, that doesn't make sense with the world I'm trying to portray," and house-rule it.
However, I think things work better if players are allowed to adjudicate their own restrictions
In my games, I leave the details of behavioral restrictions imposed by a class up to their player - the player of a paladin gets to decide what would or would not violate their oath, for example. I rarely overrule anyone, but if their interpretation of a restriction wildly differs from mine, I would certainly talk to them about it.
I think it is better for the game if a player is never surprised by their behavioral restrictions. After all, their PC should be the expert in their own oaths, so I don't want to create a situation where the PC would be wrong about them.
