There is no way around that. BridgePal needs access to the PBN file if you wish to be able to use any hand record related functionality, such as lead card validation or being able to view hand records and makeable contracts on the BridgePal scoring units.
Many clubs have their own dealing machines, in which case the person dealing the boards is likely to be a player. Even if you get someone external to the club to deal the boards, at some point the physical boards will be given to a club member for use in the session and at that time it would be possible for that person to look at the boards. In the end it comes down to trust.
The validation is certainly a very useful feature. I've been told of instances where it has enabled clubs to detect a hand misboarded part way through a session before too much damage is done.