Quite possibly. Once they have fixed the issue and removed any problem code, I would do the following:
1) Scan you personal computer using a good virus checker. If it spots anything, remove it and scan again to make sure.
2) Then log into your websites control panels and change all the passwords. Make them something good (e.g. jh38ehrkejfws9) that is not going to be guessable, don't use dictionary words. Maybe download something like Keypass,
http://keepass.info/ to keep all your passwords safe so you don't have to remember them. Passwords I would change are: FTP, CMS password and Hosting Control Panel password (if you have one). If you can't do this yourself, ask your develoer to do it for you.
3) Find out what applications your website uses and make sure you are using the latest version of each. If not have them updated (I would take advice from your developer on this to make sure nothing breaks during the update).
4) Contact your hosting company and get them to restrict FTP access and access to your various control panels to your IP. This means that only someone connectoing from your computer will get to the panel, everyone else will see a blank screen.
Essentially if you follow all the above it will make things very difficult for anyone wanting to compromise your website. Very little you can do to make it impossible but that should keep you secure. Hope that all helps (and makes sense

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