It's very unlikely that you have been banned from Croatia. I don't know much about their rules and practices but in principle they should be modelled after those of the Schengen area and there is no reason that being refused entry would result in an automatic ban or even significant difficulties for your next visit (provided you do secure a visa in advance this time).
Even overstaying (as long as it's not too long and you are leaving of your own accord) or having your visa revoked or annulled does not necessarily result in a formal ban. All these events might however make obtaining a visa or gaining entry more difficult in the future.
Furthermore, the Austrian embassy certainly does not have the authority to ban you from Croatia. What Austria could theoretically do is ban you from the whole Schengen area (and it's possible that Croatian border guards have access to the relevant database as well, since the country is in the process of joining the Schengen system but I don't really know) but, judging by your description, that's extremely unlikely to have happened until now (otherwise you would not be in Slovenia right now).
What you should however worry about is your current status in Slovenia. You now have an exit stamp and your original single-entry visa does not appear to be valid anymore so you might presently be illegally in the Schengen area. It's possible that what the Austrian embassy will tell you is that you are required to leave as soon as possible (to be honest I am a bit surprised that Slovenian border guards did not do anything about the situation, either warning you, cancelling their stamp, issuing a new visa or even detaining you; anything else than simply letting you back in with a spent visa!)
You can in any event visit Croatia in the future, even with a single-entry Schengen visa or without any Schengen visa… by applying for a Croatian visa. I doubt that you will be able to do it now without returning to your country of residence but you need to contact a Croatian embassy or consulate (and not the Austrian embassy!) for that.
The advice you received from the Croatian border guards is also very puzzling: Austria has no reason to issue a different visa because you intend to go to Croatia and is even less likely to do it now that you are already inside the Schengen area. Until Croatia joins the Schengen area and if you don't already have a multiple-entry Schengen visa for other reasons, applying for a Croatian visa would be the proper way to go about visiting the country.