Bitcoin being seized
The bitcoins on SilkRoad have been seized by gaining access to the private keys of the SilkRoad's wallets. Government agencies have seized bitcoins once before in a similar fashion from a customer of SilkRoad. $3.6m are somewhere around 30k Bitcoin out of the around 11.75m currently existing. For comparison more than 500k BTC have been transmitted in the last 24h according to Blockchain.info. The amount that was seized is economically insignificant and as it probably will be held as evidence for the trial, will not have any influence on the bitcoin market itself.
SilkRoad being shut-down
Bitcoin has plenty of legitimate reasons to be used, so that this one illegal reason should not be all that important.
Bitcoin is useful for/because:
- International money transfers (superior speed, reduced cost, however you have the currency risk)
- Faster and cheaper for shop owners compared to credit card payments
- No exposure of credit-card information when online-shopping
- Solves a bunch of problems for services such as porn merchants (no chargeback (buyer's remorse is a big problem for them), pseudonymity, fast, cheap, easy)
Bitcoin has started building a lobby (Bitcoin Foundation, Angle Investors, Investment Trusts, Exchange Traded Funds) and businesses (Exchanges, Webstores, Mining equipment manufacturers, Gambling) have been gathering investments, so that there is funded interest to keep bitcoin going.
I don't think that it was particularly unexpected to see SilkRoad shut down and don't think that it will be a bad thing for the bitcoin project. If anything, it might prove to be an opportunity for the bitcoin project to show that it has evolved beyond just shady use-cases.