Eugene Bopp's goal five minutes from time, coupled with Crewe's 2-1 win over Coventry, sent the Gills down.
Hope joined Gillingham, who he is contracted to until 2006, from United in a £250,000 move following the Iron's relegation from Division Two.
He had captained the Iron to success in the 1999 play-off final, and had spent seven seasons in North Lincolnshire after joining from Nottingham Forest.
He has played in 38 games for the Gills this season, but was not in the side at the City Ground on Sunday.
Gillingham's relegation means the League One lineup for next season is confirmed barring the winner of the League Two and League One play-offs.
Next season, United will play:
Gillingham, Nottingham Forest, Rotherham (relegated from Championship)
Three from Tranmere, Brentford, Sheff Wed and Hartlepool (who contest the League One play-offs)
Bristol City, Bournemouth, Huddersfield, Doncaster, Bradford, Swindon, Barnsley, Walsall, Colchester, Blackpool, Chesterfield, Port Vale, Oldham and Franchise FC.
Yeovil and Swansea (promoted from League Two, along with the Iron)
Southend, Macclesfield, Lincoln or Northampton (who contest the League Two play-offs)