Then you don't agree. If the DM is not making the game run smoothly*, then basically the DM is saying, "Alright, you play what makes you happy, but I'm going to make your life difficult, and possibly kill you. Too bad."
Umm. I really dislike what you seem to imply here. There's a world of difference between a DM going out of his way to make life difficult for the pcs and telling the players that they may have a more difficult time because of their choices if they don't take their weaknesses (like missing a role) into account.
Take your hypothetical example of an all Rogue party. There will be obvious, possible extreme tactical difficulties with such a party, I don't disagree on that part. In fact, my guess would be that such a party would be relatively unsustainable (though now I'm curious). However, everyone is (in theory) playing what they want to play. It's the DM's job then to prevent it being a TPK.
Well, I guess it's possible to play a campaign with such a party but it would be a completely different campaign than one with a party covering all of the roles. This is fine if either the DM doesn't care, or it's what the players and DM agreed on beforehand. It's not fine if the players and the DM decided the campaign was going to be a 'standard' campaign.
I like the advice the DMG gives on page 10:
When players are making new characters, they should discuss their preferences in roles, and agree on how to cover all the roles[...]Otherwise, you might end up with a party of five strikers.
Take a more real example - no one wants to play a leader. The party should be punished by that lack of a role (healing/support) because no one wants to play a character they don't want to?
That shouldn't be a problem. Again, the appropriate advice can be found on page 10 in the DMG. As a DM I'd just spell out to them what the section on 'No Leader' says.
*Smoothly (wrt combat) does not mean easily; smoothly means not every combat is a near-TPK or an exercise in frustration.
As I mentioned above there's three ways to react to a party with a non-standard composition:
1) Go out of your way to make things easier for the pcs by avoiding encounters that become more difficult if a certain role is missing - this seems to be your preference.
2) Go out of your way to make things more difficult for the pcs by focusing on encounters that become more difficult if a certain role is missing - this seems to be only other option you see.
3) Don't change anything. Use the suggestions for building encounters straight from the DMG.
Obviously, I'm a proponent of option 3).
I trust my players to be sufficiently creative and clever to deal with standard encounters even with a non-standard party setup. It might be more difficult at times but some players (including mine) enjoy the challenge.