The fact that not all Amazon employees approve of the lobbying is irrelevant. Not all union members approve of all the union lobbying done. Should we silence unions? Not all members of a political party approve of all the positions taken by political parties. Should we silence political parties? When people join up into groups, they trade increased power for the fact that the group will not perfectly reflect their preferences.
It surely is the case that lots of people who work at Amazon want Amazon to continue to lobby for things that will help Amazon become more valuable, thus making it less likely they will be laid off and making their equity more valuable.
In what way is the world better if Amazon increases Jeff Bezos' salary by $AMOUNT_THEY_SPEND_ON_LOBBYING and then Jeff Bezos spends that money on lobbying for whatever he wants, which surely includes "making Amazon successful"? Even if Amazon rigorously does not direct him to spend that money or audit his efforts?
I'm fine with foreign companies lobbying the government. Why wouldn't I be?