If distributed attacks on web analytics become common place, those of us doing SEO are in for a world of hurt... After all, how can you prove your worth if your statistics can't be relied on? But, while painful, botnet analytics hacking really isn't the end of SEO - let me explain...
Insuring that pages are built correctly
At it's heart, one of the core practices of SEO is to ensure that pages are built properly - that their focus and content can be easily understood by search engine spiders. "Web designers" just want pages to look pretty. "Web programmers" just want pages to be connected to data sources in cool ways or do some other cool trick. Neither of those groups really cares about how the pages perform. SEO will always need to be there to make sure the page can be understood by search engines. With the advent of botnet web analytics corruption, it may be difficult for an SEOer to prove s/he's done her/his job, but it's not impossible...
Sites that have e-commerce as their primary goal will be far less affected than "marketing" sites trying to get market exposure because e-commerce transactions will be difficult to fake. Conversion ratios may be corrupted, but the actual sales (in dollars, pounds, euros, etc.) will still be a concrete measure of success. Further, segmentation by things like "paying customer" will become invaluable.
Building on segmentation possible with e-commerce, segmentation based on whether the user is registered will be invaluable as well. Using segmentation, you can look just at the activity of registered users which should be bot free provided you use a good captcha, and possibly e-mail confirmation. (At the very least it will take a very targeted attack to mess with your user segmentation data - it won't be affected by random attacks).
Ranking in SERPs
Your actual ranking in the SERPs is also something that can't be faked. Programs like WebPosition, while hated by the search engines, will be critical in measuring success and validating organic traffic. [If you're getting traffic off the keyword 'art', but don't rank for 'art', then you know you have a bot problem.]
The cost of good analytics
The analytics company that works the hardest to combat botnets will be the big winner here. Since Google Analytics, Microsoft Gatineau, and now IndexTools (Yahoo!), are free packages it's unclear whether Google, Microsoft or Yahoo! really have the incentive to combat the effects of botnets. I mean, look at Google's track record with click fraud in AdWords. Even if you accept the fact that they try to stop it, there's still plenty of it that goes undetected. If the tool that is best able to effectively detect and squash botnets is a paid service, there will be a very real increase in the cost of quality analytics.
It will also be more expensive to interpret analytics since you can't just take the numbers at face value. You'll have to jump through more hoops to come to a conclusion and it's not likely to be able to be done by people without significant experience. Those experts will come at a price.
I can also see 3rd party verification services cropping up that may not engage in SEO, but validate the results of SEO companies. Again, an added cost, though probably only something that would be done for very high-end projects.
Botnets aren't going to destroy the SEO industry. If anything they'll increase the level of professionalism. Word will get out that fraud and deception are possible with SEO and reputation will become absolutely critical. I'm guessing it will knock some smaller players (both customers and providers) out of the game - or at least knock them down to a place where they don't even try to validate results. But in cases where money talks, money will be able to buy at least "decent" analytics and the people who are best qualified to interpret the data.
Still, analytics hacking by botnets will become a much bigger problem in the future, and it will radically change the SEO industry...