Your problem I think is a matter of three things. The first being that a charachter should be built with a concept and be built to show it. The second is the rules tell approximately how they should be handled. Thirdly, it looks like the particular issue shows he is trying to get more than the points allow for.
I would suggest putting together packages for types of charachters you expect. It allows players to see what is involved with being a certain class. With the noble example they would probably have higher EGO and PRE scores because of their background. They should have several supporting skills like High Society and Conversation, in addition to KS's. They might have a required disadvantage, such as Vassal to Lord. They may well have several contacts. If you know what it is that the players will be playing you can make story lines around it.
The Fifth Ed. and Fantasy Hero explain how Perks are handled and why the costs are so low. In the Fifth it states that most Perks can be nullified through play without the points being returned (effectively making them Independent). Also that a Perk comes with advantage and disadvantage. "being a member of a group means the character also has responsibilities to that group (as reflected by related Disadvantages...)" Hero System Fifth Edition pg 58. In Fantasy Hero it goes on to list the responsibilities of a lord on page 99.
To be a full Lord you must spend more than just three points to gain all of the advantages you listed. To have that kind of power you are looking at High King or Emperor (20 points). Let's look at each item.
"-- ordering commoners to fight for him"
Commoners might fight if the enemy was also threatening his livelihood but are just as likely to flee in terror. Judge the situation and determine what their reaction would be. A lord should already have a standing army of some sort to do that sort of thing. Maybe he should buy a follower and have it changeable to any nearby loyal commoner.
"-- ordering people to surrender"
I don't understand the problem here. If they are committing some crime where he will punish them if they surrender, then they won't.
"-- ignoring laws by being above them, and being immune from punishment"
He should be able to do this in his own area, although, that's a sure way to make sure that there is some sort of rebellion from the masses no matter how high his rank.
"-- license to kill; to render low justice on the spot"
He should be able to do this in his own area, although, that's a sure way to make sure that there is some sort of rebellion from the masses no matter how high his rank.
"-- getting bonuses to presence, influence, negotiations, etc."
These could be possible depending on situation.
I hope this helps.