This discussion seems to say that defining interop legacy settings is a workaround (instead of going back to an older version that works... http://www.mail-archive.com/sqlite-users%40sqlite.org/msg75310.html
"
The root cause in this case is that the Entity Framework indirectly creates a
SQLiteCommand object and then subsequently fails to dispose it.
Furthermore, it does not appear to expose these internally created commands, nor a way to explicitly dispose of them, leaving no means for an outside caller to cleanup. This seems quite strange since almost all IDbCommand implementations "in the wild" would likely require native resources of one kind or another. Also, even the DbCommand base class provided by the .NET Framework itself implements IDisposable (i.e. the class used as the base class for SQLiteCommand).
"
"
Yes, the InteropLegacyClose MSBuild property in the "SQLite.NET.Settings.targets" file needs to be set to "true" and the define "INTEROP_LEGACY_CLOSE=1;" needs to be added to the INTEROP_EXTRA_DEFINES property in the SQLite.Interop.20XX.[vs]props file for the version of Visual Studio being used.
"
UPDATE: dotConnect for SQLLite looks the business http://www.devart.com/dotconnect/sqlite/ there is a free and pro version which isn't free... might be worth checking it out.
UPDATE2: In response to " If this was a bug with EF, everyone that uses it would have issues even when targeting SQL Server. – Panagiotis Kanavos"
Not at all, it seems the bug is only reported by SQLLite users around 1.0.8xxx where they changed their dispose methods... the EF provider can vary, e.g. you could set it to SQLLite (bug reported) or SQLServer (bug not reported) etc like below...
<system.data>
<DbProviderFactories>
<add name="SQLite Data Provider"
invariant="System.Data.SQLite"
description="Data Provider for SQLite"
type="System.Data.SQLite.SQLiteFactory, System.Data.SQLite" />
</DbProviderFactories>
</system.data>
or
<providers>
<provider invariantName="System.Data.SqlClient" type="System.Data.Entity.SqlServer.SqlProviderServices, EntityFramework.SqlServer" />
</providers>