@Kaarme and partially
@mahtan (A bit long but this is to clarify some things)
She's, at the moment, the acting lord, she's acting as a proxy for her father, she's using HIS power not her own. She's already been banished from noble society and hasn't been allowed back in yet. She has no official noble title, she's simply a Duke's daughter, and in noble society, she has no power outside of being a proxy. Any decisions she makes as acting lord of the fief reflects back to him as if he was the one who decided such actions since he is the one who officially holds the power as a Duke and as a lord of a fief.
The church having denounced her for her act of tearing down a church. Because she's the acting lord of the fief, her father is one being inquired, not her. Since he doesn't know everything of what she did as acting lord, unopposed the inquiry will find him negligent in his duties and make him step down from being Prime Minister while making him take responsibility for her actions. She's more or less just a daughter of a Duke that has no real power or the proper connections to defend herself.
What advantages she may have done for her fief are insignificant as it is only for her fief, the other fiefs are unaffected and will not follow her example, especially the 2nd prince faction ones. Against the accusation of committing a sacrilegious act of tearing down a church without permission, the corrupt priests from who knows where in the hierarchy, probably pretty high, will align with the 2nd prince faction's goals to stay in the "winning" faction's good graces. Which is more advantageous to them, a mere Duke's daughter with no power or the next ruler of the kingdom.
The tolls placed against the fief causes her to try and find other routes that are SLIGHTLY less expensive to deal with but she is still facing a loss. More overhead she has to deal with the fewer profits she can use for investing in other ventures or even the same ventures. And it takes more time which means more perishable products might not survive the longer journey. Remember there's no such thing as mobile refrigeration technology and they are using horses and carriages. In this world, the route she was using was the fastest and most expedient route she could use. If she's forced to take a longer and more dangerous route while also compensating it in other areas like extra hired guards. She has to spend more money to deal with it and fewer products that might still be sellable. And it's not easy to raise prices for her products if her reputation is also in question. And there's also the number of tolls she would have to go through if she DID do so, and whether or not they'll raise them again against her.