It's possible to make perfectly fair monetization systems, which do affect gameplay. Selling telecrystals for money would obviously be a horrible idea, but there are things you could sell. I know they are considered a joke here, but selling something like antag tokens in a clever way could work and potentially even improve the game.
Now I know you are probably experiencing a knee-jerk reaction and are foaming at the mouth already, let me begin by saying this is nothing more than a thought experiment. I doubt the current admin/coder team would be willing to put through with the backlash that something like this would cause and would likely rather go through a full server shutdown than have to deal with the hot heads of TGS for a few months, before they realized how innocuous it actually would be.
Anyway, disclaimer over, selling something like antag tokens would have to come with limits on their use. Because there is a finite number of antags that can be distributed and you definitely don't want paid antags to become anywhere near the majority. So you could find out how often a player is expected to play an antag, and allow players to use a token only this often. So say that comes up as "on average, each player plays an antag once per week", well then you only allow players to use one antag token per week. On top of this, you limit it to some percentage of antags - for example, only 2 of the 8 traitors in a round can come from antag tokens, even if more people want to use tokens that round.
By adding all these conditions and limits, the game remains perfectly fair for non-paying players, the tokens can be cheap and you have lots of parameters you can tweak if the situation changes (for example if too many people start buying tokens). In most games, the only parameter you can tweak is the sale price. Here you can tweak lots of much easier-to-tweak things.
Just a brief mention though: There are benefits that systems of this sort can bring - specifically by making games more available to players with less time. For example, if you can only play a game or two per week, you'd likely want to play that game as an antag. A token could ensure that with negligible impact on non-paying players and a monetary benefit to the server host (which in turn benefits non-paying players). This obviously assumes the system was well designed and fair. I don't know how big an impact this would have on SS13, but I did want to mention this. And while some MMOs and mobile games also cite this as a benefit, they are only really in it for the money. Here, the system could actually be designed to optimize for the benefit of having more players with less time play.
Please don't take this post as a suggestion, idea or anything of the sort. It's merely a thought experiment. The truth would obviously not be as rosy as this post might make it seem, but it would also not be as dystopian as that knee jerk reaction you experienced at the start of this post would have you think. The truth would be somewhere in the middle... but at least the server would be funded