Sure they can. They can't get rid of the protocol, but they can make it useless.
Let's say for you have a totalitarian country.
They can make a law saying that they'll execute anyone who uses bitcoin. Nobody would dare touch it anymore. That's an extreme, but it's still possible in some countries (more realistically they'd seize your assets).
Just to be clear, you state suppositions, none of this has happened.
- Give it unfavorable tax treatment
The last move by the IRS gives preferential tax treatment for long term capital gains, but not good for miners that mined at a high BTC price and sold at a lower price. In essence, they did not realize they were speculating between mining and realizing the profit.
- Force merchants who accept it to adhere to complex and expensive accounting rules, so that it's not economical to accept it as payment for any legitimate business
This is silly. You are supposing that a merchant has the technology to accept bitcoin, but is unable to keep track of bitcoin sales and access historical price data. They have apps for that.
- Call it a counterfeit currency and prosecute people who try to use it. (2 words: Liberty Dollar). I don't care if you want to believe it or not, but if you print up your own money (even if it doesn't resemble US dollars at all, eg. Bitcoin bills), go to a store, and try to pay with it you CAN get in trouble.
This was a centralized money system run by people with strong anti-government views. I'm not saying it was right to prosecute them, but they made themselves a target.
- Make a few high profile examples. Find a company doing bitcoin mining who's books aren't correct to the letter, seize their assets. Find a bitcoin user who didn't report capital gains on their coins and throw them in jail for tax evasion.
This is a supposition with no evidence that it's going to happen. Currently, the IRS has been starved of money by conservative forces in the government, which prevents them from collecting a lot of taxes (even though stronger enforcement would bring in more revenue than would be spent on enforcement.) According to IRS statistics, the chance that a person making 50K-70K a year has a 0.7% chance of a tax return (or a non-existent tax return with reported W2 or 1099 income) being examined. Over 5 years, that's about a 3.1% chance of getting caught.
- Use the fact that bitcoin is commonly used for criminal purposes to have law enforcement harass bitcoin users. Government can seize coins that are traced to have been used in illegal activity (or if the government SUSPECTS they were used in illegal activity). This can easily be done to merchants by mandating they report transactions and wallet addresses. The govt could even go a step further and mandate that merchants give access (private key) to those wallets to a govt agency.
In regards to illegal activities, many jurisdictions (as a revenue generating procedure) will seize large amounts of cash from travelers on interstate highways as suspected drug money. This is nothing new, and nothing inherent to bitcoin.
In reality, the majority of merchants will convert immediately to fiat and not speculate on bitcoin. The government is more likely to give merchants a Cyprus-style haircut through their bank accounts than to demand direct access to any bitcoins they hold. Cyprus haircuts would be very unpopular, and in the United States, the history has been to support sick financial institutions by selling T-bills to prop them up (taxing dollar holders in a non-obvious way)
Supporting legitimate business using bitcoin is the way to go, to reduce the stigma of illegal activity, which makes it harder for the government to use the "illegal activities" excuse to crackdown on bitcoin.
Sure, things like drugs are illegal and are a thriving economy, but that's different. You can't grind up a bitcoin, snort it, and get high, so if the government hassles people who use it, and no legitimate business will accept it because it's too much of a pain in the ass, nobody is going to bother using it unless they want to use it to buy drugs online or something.
Even if the government totally cracked down on bitcoin, there would still be a bitcoin economy -- street level bitcoin dealers that traded bitcoins for cash to users that gambled and bought drugs through the internet.
I see the future of bitcoin as positive, as legitimate money is being invested in bitcoin services and merchants. It will reach a tipping point where it becomes a significant portion of the legitimate economy, where a crackdown would cause harm to the country as a whole.