I think they have a place in F1 if used appropriately. It's a team sport.
I generally think teams do use them appropriately. There aren't too many orders I've disagreed with. I think it's also interesting that we (IMO) see about the same amount of use of team orders, whether they are banned or not (albeit the orders were less explicit during the ban) - which I think is further evidence that the teams use them appropriately.
Examples of where I think it's ok (and think most people have a similar view) would include:
1. WDC at stake, one driver mathematically out
2. Two drivers on a different strategy, driver on the "quicker" part of his strategy is behind, and other cars are being raced (ie the two aren't miles in front in a guaranteed 1/2)
3. One driver is very clearly, and significantly, quicker than the other (even though on the same strategy) and there are places ahead that the team could pick up
4. A result is in the bag, fighting between the 2 drivers only puts that at risk for no potential gain and "hold positions" is issued
I'm also ok with 2004 Austria and 2010 Germany style (team mate isn't out of the WDC, but it is absolutely clear based on past form which of the team's drivers is going to be their best chance of a WDC).
In this example, I didn't think TR were right to issue the order and I think Max was right to refuse it. I think similarly for Hungary 14 between Hamilton and Rosberg and Malaysia 14 for Massa and Bottas.
I thought Vettel was right to refuse the Multi-21 order, but that was on the basis the other driver was Webber who had ignored the same order in the past when the roles were reversed, rather than because RBR were wrong to issue the order.