Most often than not, the scheme of the website has to match that of the logo. When the logo has a RED, on a page it becomes unavoidable not to have a RED colored alerts, warnings, error messages displayed. Some times, initial message itself could have certain alerts to be displayed and that floods the site with RED, AMBER. Too many colors increase friction and reduce the user experience. Question: is there an alternate set of colors that can be used and break away from traditional colors? And by doing so, will the overall usability increase / decrease? Thoughts with research/real experience siting are most welcome. Thank you
Using red for alerts and warnings can be tricky in general. A nice and short article about this is written by David Walsch: http://davidwalsh.name/dont-be-a-f00. In depth information about the systems tone of voice to users can be found in the book About Face 3 by Alan Cooper (a must read btw). One of the general rules is to don't let users feel stupid so try avoid combinations like 'you've made an error'.
For a solution to your problem I would look at other graphic possibilities than color. For example: you could place the message within a box that has a different background and/or border. Or you could make all system notifications italic for example. The most important thing, in my opinion, is that the notifications are easily recognized. It's therefor more important that the notifications are part of a coherent system, than that they are red.